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@article{DBLP:journals/jcamd/ClevesJDBWH24,
author = {Ann E. Cleves and
Ajay N. Jain and
David A. Demeter and
Zachary A. Buchan and
Jeremy Wilmot and
Erin N. Hancock},
title = {From {UK-2A} to florylpicoxamid: Active learning to identify a mimic
of a macrocyclic natural product},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {19},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00555-3},
doi = {10.1007/S10822-024-00555-3},
timestamp = {Fri, 17 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ClevesJDBWH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DanilackDSFRMHD24,
author = {Aaron D. Danilack and
Callum J. Dickson and
Cihan Soylu and
Mike Fortunato and
Stephane Rodde and
Hagen Munkler and
Viktor Hornak and
Jos{\'{e}} S. Duca},
title = {Reactivities of acrylamide warheads toward cysteine targets: a {QM/ML}
approach to covalent inhibitor design},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {21},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00560-6},
doi = {10.1007/S10822-024-00560-6},
timestamp = {Wed, 08 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DanilackDSFRMHD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Elseginy24,
author = {Samia A. Elseginy},
title = {Identifying and characterising promising small molecule inhibitors
of kinesin spindle protein using ligand-based virtual screening, molecular
docking, molecular dynamics and MM{\unicode{8209}}GBSA calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {16},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00553-5},
doi = {10.1007/S10822-024-00553-5},
timestamp = {Mon, 15 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Elseginy24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FuhrerGDGMS24,
author = {Florian F{\"{u}}hrer and
Andrea Gruber and
Holger Diedam and
Andreas H. G{\"{o}}ller and
Stephan Menz and
Sebastian Schneckener},
title = {A deep neural network: mechanistic hybrid model to predict pharmacokinetics
in rat},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {7},
year = {2024},
url = {https://doi.org/10.1007/s10822-023-00547-9},
doi = {10.1007/S10822-023-00547-9},
timestamp = {Tue, 20 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/FuhrerGDGMS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GallardoD24,
author = {Adan Gallardo and
Bercem Dutagaci},
title = {Binding of small molecule inhibitors to {RNA} polymerase-Spt5 complex
impacts {RNA} and {DNA} stability},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {1},
year = {2024},
url = {https://doi.org/10.1007/s10822-023-00543-z},
doi = {10.1007/S10822-023-00543-Z},
timestamp = {Sun, 10 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GallardoD24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HalipACBBBO24,
author = {Liliana Halip and
Sorin I. Avram and
Ramona Curpan and
Ana Borota and
Alina Bora and
Cristian Bologa and
Tudor I. Oprea},
title = {Correction: Exploring DrugCentral: from molecular structures to clinical
effects},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {2},
year = {2024},
url = {https://doi.org/10.1007/s10822-023-00545-x},
doi = {10.1007/S10822-023-00545-X},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/HalipACBBBO24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HonigFENSLR24,
author = {Sophia M. N. H{\"{o}}nig and
Florian Flachsenberg and
Christiane Ehrt and
Alexander Neumann and
Robert Schmidt and
Christian Lemmen and
Matthias Rarey},
title = {SpaceGrow: efficient shape-based virtual screening of billion-sized
combinatorial fragment spaces},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {13},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00551-7},
doi = {10.1007/S10822-024-00551-7},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HonigFENSLR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JainBJCKCM24,
author = {Ajay N. Jain and
Alexander C. Brueckner and
Christine Jorge and
Ann E. Cleves and
Purnima Khandelwal and
Janet Caceres Cortes and
Luciano Mueller},
title = {Correction: Complex peptide macrocycle optimization: combining {NMR}
restraints with conformational analysis to guide structure-based and
ligand-based design},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {12},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00556-2},
doi = {10.1007/S10822-024-00556-2},
timestamp = {Mon, 15 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/JainBJCKCM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JonesCLMW24,
author = {Jeremy Jones and
Robert D. Clark and
Michael S. Lawless and
David W. Miller and
Marvin Waldman},
title = {The AI-driven Drug Design {(AIDD)} platform: an interactive multi-parameter
optimization system integrating molecular evolution with physiologically
based pharmacokinetic simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {14},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00552-6},
doi = {10.1007/S10822-024-00552-6},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/JonesCLMW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KabedevBL24,
author = {Aleksei Kabedev and
Christel A. S. Bergstr{\"{o}}m and
Per Larsson},
title = {Molecular dynamics study on micelle-small molecule interactions: developing
a strategy for an extensive comparison},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {5},
year = {2024},
url = {https://doi.org/10.1007/s10822-023-00541-1},
doi = {10.1007/S10822-023-00541-1},
timestamp = {Mon, 15 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KabedevBL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LazouHCJ24,
author = {Maria Lazou and
Jonathan R. Hutton and
Arijit Chakravarty and
Diane Joseph{-}McCarthy},
title = {Identification of a druggable site on {GRP78} at the GRP78-SARS-CoV-2
interface and virtual screening of compounds to disrupt that interface},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {6},
year = {2024},
url = {https://doi.org/10.1007/s10822-023-00546-w},
doi = {10.1007/S10822-023-00546-W},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LazouHCJ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/McNuttK24,
author = {Andrew T. McNutt and
David Ryan Koes},
title = {Open-ComBind: harnessing unlabeled data for improved binding pose
prediction},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {3},
year = {2024},
url = {https://doi.org/10.1007/s10822-023-00544-y},
doi = {10.1007/S10822-023-00544-Y},
timestamp = {Wed, 20 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/McNuttK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MoraMPCPAMMB24,
author = {Jos{\'{e}} Ram{\'{o}}n Mora and
Edgar M{\'{a}}rquez and
Noel P{\'{e}}rez{-}P{\'{e}}rez and
Ernesto Contreras{-}Torres and
Yunierkis P{\'{e}}rez{-}Castillo and
Guillerm{\'{\i}}n Ag{\"{u}}ero{-}Chap{\'{\i}}n and
Felix Martinez{-}Rios and
Yovani Marrero{-}Ponce and
Stephen J. Barigye},
title = {Rethinking the applicability domain analysis in {QSAR} models},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {9},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00550-8},
doi = {10.1007/S10822-024-00550-8},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MoraMPCPAMMB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NesabiKRGB24,
author = {Azam Nesabi and
Jas Kalayan and
Sara Al Rawashdeh and
Mohammad A. Ghattas and
Richard A. Bryce},
title = {Molecular dynamics simulations as a guide for modulating small molecule
aggregation},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {11},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00557-1},
doi = {10.1007/S10822-024-00557-1},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NesabiKRGB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PennerV24,
author = {Patrick Penner and
Anna Vulpetti},
title = {{QM} assisted {ML} for \({}^{\mbox{19}}\)F {NMR} chemical shift prediction},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {4},
year = {2024},
url = {https://doi.org/10.1007/s10822-023-00542-0},
doi = {10.1007/S10822-023-00542-0},
timestamp = {Sun, 31 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/PennerV24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ScalzittiMKFGB24,
author = {Nicolas Scalzitti and
Iliya Miralavy and
David E. Korenchan and
Christian T. Farrar and
Assaf A. Gilad and
Wolfgang Banzhaf},
title = {Computational peptide discovery with a genetic programming approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {17},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00558-0},
doi = {10.1007/S10822-024-00558-0},
timestamp = {Mon, 15 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ScalzittiMKFGB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SkSPK24,
author = {Md Fulbabu Sk and
Sunanda Samanta and
Sayan Poddar and
Parimal Kar},
title = {Deciphering the molecular choreography of Janus kinase 2 inhibition
via Gaussian accelerated molecular dynamics simulations: a dynamic
odyssey},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {8},
year = {2024},
url = {https://doi.org/10.1007/s10822-023-00548-8},
doi = {10.1007/S10822-023-00548-8},
timestamp = {Thu, 29 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SkSPK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VazquezGLLH24,
author = {Javier V{\'{a}}zquez and
Ricardo Garc{\'{\i}}a and
Paula Llinares and
F. Javier Luque and
Enric Herrero},
title = {On the relevance of query definition in the performance of 3D ligand-based
virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {18},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00561-5},
doi = {10.1007/S10822-024-00561-5},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VazquezGLLH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Ye24,
author = {Gavin Ye},
title = {De novo drug design as {GPT} language modeling: large chemistry models
with supervised and reinforcement learning},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {20},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00559-z},
doi = {10.1007/S10822-024-00559-Z},
timestamp = {Wed, 08 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Ye24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZenginKTYK24,
author = {Irem N. Zengin and
M. Serdar Koca and
Omer Tayfuroglu and
Muslum Yildiz and
Abdulkadir Kocak},
title = {Benchmarking {ANI} potentials as a rescoring function and screening
{FDA} drugs for SARS-CoV-2 M\({}^{\mbox{pro}}\)},
journal = {J. Comput. Aided Mol. Des.},
volume = {38},
number = {1},
pages = {15},
year = {2024},
url = {https://doi.org/10.1007/s10822-024-00554-4},
doi = {10.1007/S10822-024-00554-4},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZenginKTYK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BjerrumMBKC23,
author = {Esben Jannik Bjerrum and
Christian Margreitter and
Thomas Blaschke and
Simona Kolarova and
Raquel Lopez{-}Rios de Castro},
title = {Faster and more diverse de novo molecular optimization with double-loop
reinforcement learning using augmented {SMILES}},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {8},
pages = {373--394},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00512-6},
doi = {10.1007/S10822-023-00512-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BjerrumMBKC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BoninMNG23,
author = {Anne Bonin and
Floriane Montanari and
Sebastian Niederf{\"{u}}hr and
Andreas H. G{\"{o}}ller},
title = {pH-dependent solubility prediction for optimized drug absorption and
compound uptake by plants},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {3},
pages = {129--145},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00496-3},
doi = {10.1007/S10822-023-00496-3},
timestamp = {Thu, 09 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/BoninMNG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CarneiroMRSPS23,
author = {Jo{\~{a}}o Carneiro and
Rita P. Magalh{\~{a}}es and
Victor M. de la Oliva Roque and
Manuel Sim{\~{o}}es and
Diogo Pratas and
Sergio F. Sousa},
title = {TargIDe: a machine-learning workflow for target identification of
molecules with antibiofilm activity against Pseudomonas aeruginosa},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {5},
pages = {265--278},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00505-5},
doi = {10.1007/S10822-023-00505-5},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CarneiroMRSPS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChoiLCCPHLH23,
author = {Jiwon Choi and
Hyundo Lee and
Soyoung Cho and
Yorim Choi and
Thuy X. Pham and
Trang T. X. Huynh and
Yun{-}Sook Lim and
Soon B. Hwang},
title = {Polygalic acid inhibits african swine fever virus polymerase activity:
findings from machine learning and in vitro testing},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {9},
pages = {453--461},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00520-6},
doi = {10.1007/S10822-023-00520-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChoiLCCPHLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DiedenhofenET23,
author = {Michael Diedenhofen and
Frank Eckert and
Selman Terzi},
title = {{COSMO-RS} blind prediction of distribution coefficients and aqueous
pKa values from the {SAMPL8} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {8},
pages = {395--405},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00514-4},
doi = {10.1007/S10822-023-00514-4},
timestamp = {Fri, 21 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DiedenhofenET23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DiedrichKBR23,
author = {Konrad Diedrich and
Bennet Krause and
Ole Berg and
Matthias Rarey},
title = {PoseEdit: enhanced ligand binding mode communication by interactive
2D diagrams},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {10},
pages = {491--503},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00522-4},
doi = {10.1007/S10822-023-00522-4},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DiedrichKBR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FreitasRAHPCSBMBBT23,
author = {Talita Freitas de Freitas and
Candida Deves Roth and
Bruno Lopes Abbadi and
Fernanda Souza Macchi Hopf and
Marcia Alberton Perell{\'{o}} and
Alexia de Matos Czeczot and
Eduardo Vieira de Souza and
Ana Fl{\'{a}}via Borsoi and
Pablo Machado and
Cristiano Valim Bizarro and
Luiz Augusto Basso and
Lu{\'{\i}}s Fernando S. M. Timmers},
title = {Identification of potential inhibitors of Mycobacterium tuberculosis
shikimate kinase: molecular docking, in silico toxicity and in vitro
experiments},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {3},
pages = {117--128},
year = {2023},
url = {https://doi.org/10.1007/s10822-022-00495-w},
doi = {10.1007/S10822-022-00495-W},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FreitasRAHPCSBMBBT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GhetaBGG23,
author = {Sadra Kashef Ol Gheta and
Anne Bonin and
Thomas Gerlach and
Andreas H. G{\"{o}}ller},
title = {Predicting absolute aqueous solubility by applying a machine learning
model for an artificially liquid-state as proxy for the solid-state},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {765--789},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00538-w},
doi = {10.1007/S10822-023-00538-W},
timestamp = {Wed, 08 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GhetaBGG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HabiballahCMR23,
author = {Sohaib Habiballah and
Janice Chambers and
Edward Meek and
Brad Reisfeld},
title = {The in silico identification of novel broad-spectrum antidotes for
poisoning by organophosphate anticholinesterases},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {755--764},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00537-x},
doi = {10.1007/S10822-023-00537-X},
timestamp = {Wed, 08 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/HabiballahCMR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HalipACBBBO23,
author = {Liliana Halip and
Sorin I. Avram and
Ramona Curpan and
Ana Borota and
Alina Bora and
Cristian Bologa and
Tudor I. Oprea},
title = {Exploring DrugCentral: from molecular structures to clinical effects},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {681--694},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00529-x},
doi = {10.1007/S10822-023-00529-X},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HalipACBBBO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HanpaiboolOYMSNR23,
author = {Chonnikan Hanpaibool and
Puey Ounjai and
Sirilata Yotphan and
Adrian J. Mulholland and
James Spencer and
Natharin Ngamwongsatit and
Thanyada Rungrotmongkol},
title = {Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing
E. coli: an in silico and in vitro investigation},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {10},
pages = {479--489},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00519-z},
doi = {10.1007/S10822-023-00519-Z},
timestamp = {Thu, 31 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HanpaiboolOYMSNR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HeM23,
author = {Kedan He and
Djenerly G. Massena},
title = {Examining unsupervised ensemble learning using spectroscopy data of
organic compounds},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {1},
pages = {17--37},
year = {2023},
url = {https://doi.org/10.1007/s10822-022-00488-9},
doi = {10.1007/S10822-022-00488-9},
timestamp = {Tue, 31 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/HeM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HuSKC23,
author = {Jiaqi Hu and
Xianqiang Sun and
Zhengzhong Kang and
Jianxin Cheng},
title = {Computational investigation of functional water molecules in GPCRs
bound to {G} protein or arrestin},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {2},
pages = {91--105},
year = {2023},
url = {https://doi.org/10.1007/s10822-022-00492-z},
doi = {10.1007/S10822-022-00492-Z},
timestamp = {Tue, 31 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/HuSKC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JainBJCKCM23,
author = {Ajay N. Jain and
Alexander C. Brueckner and
Christine Jorge and
Ann E. Cleves and
Purnima Khandelwal and
Janet Caceres Cortes and
Luciano Mueller},
title = {Complex peptide macrocycle optimization: combining {NMR} restraints
with conformational analysis to guide structure-based and ligand-based
design},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {11},
pages = {519--535},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00524-2},
doi = {10.1007/S10822-023-00524-2},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JainBJCKCM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JaradatHAT23,
author = {Nour Jamal Jaradat and
M{\'{a}}mon M. Hatmal and
Dana Alqudah and
Mutasem Omar Taha},
title = {Computational workflow for discovering small molecular binders for
shallow binding sites by integrating molecular dynamics simulation,
pharmacophore modeling, and machine learning: {STAT3} as case study},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {659--678},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00528-y},
doi = {10.1007/S10822-023-00528-Y},
timestamp = {Fri, 10 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JaradatHAT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JaradatHAT23a,
author = {Nour Jamal Jaradat and
M{\'{a}}mon M. Hatmal and
Dana Alqudah and
Mutasem Omar Taha},
title = {Correction to: Computational workflow for discovering small molecular
binders for shallow binding sites by integrating molecular dynamics
simulation, pharmacophore modeling, and machine learning: {STAT3}
as case study},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {679},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00540-2},
doi = {10.1007/S10822-023-00540-2},
timestamp = {Wed, 08 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JaradatHAT23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JorgensenTUSU23,
author = {Christian Jorgensen and
Evan P. Troendle and
Jakob P. Ulmschneider and
Peter C. Searson and
Martin B. Ulmschneider},
title = {A least-squares-fitting procedure for an efficient preclinical ranking
of passive transport across the blood-brain barrier endothelium},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {11},
pages = {537--549},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00525-1},
doi = {10.1007/S10822-023-00525-1},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JorgensenTUSU23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiUH23,
author = {Haoxi Li and
Nikhil M. Urs and
Nicole Horenstein},
title = {Computational insights into ligand-induced {G} protein and {\(\beta\)}-arrestin
signaling of the dopamine {D1} receptor},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {5},
pages = {227--244},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00503-7},
doi = {10.1007/S10822-023-00503-7},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiUH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiangKSCDHC23,
author = {Fanglin Liang and
Zhengzhong Kang and
Xianqiang Sun and
Jiao Chen and
Xuemin Duan and
Hu He and
Jianxin Cheng},
title = {Inhibition mechanism of {MRTX1133} on KRAS\({}^{\mbox{G12D}}\): a
molecular dynamics simulation and Markov state model study},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {3},
pages = {157--166},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00498-1},
doi = {10.1007/S10822-023-00498-1},
timestamp = {Thu, 09 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LiangKSCDHC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuDLWWCL23,
author = {Bo Liu and
Juntao Ding and
Yugang Liu and
Jianzhang Wu and
Xiaoping Wu and
Qian Chen and
Wulan Li},
title = {Elucidating the potential effects of point mutations on {FGFR3} inhibitor
resistance via combined molecular dynamics simulation and community
network analysis},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {7},
pages = {325--338},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00510-8},
doi = {10.1007/S10822-023-00510-8},
timestamp = {Tue, 27 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiuDLWWCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiyaqatAS23,
author = {Tanya Liyaqat and
Tanvir Ahmad and
Chandni Saxena},
title = {TeM-DTBA: time-efficient drug target binding affinity prediction using
multiple modalities with Lasso feature selection},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {573--584},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00533-1},
doi = {10.1007/S10822-023-00533-1},
timestamp = {Wed, 08 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LiyaqatAS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LlanosARSMPFCSGT23,
author = {Manuel A. Llanos and
Lucas N. Alberca and
Mar{\'{\i}}a D. Ruiz and
Mar{\'{\i}}a L. Sbaraglini and
Cristian Miranda and
Agustina Pino{-}Martinez and
Laura Fraccaroli and
Carolina Carrillo and
Catalina D. Alba Soto and
Luciana Gavernet and
Alan Talevi},
title = {A combined ligand and target-based virtual screening strategy to repurpose
drugs as putrescine uptake inhibitors with trypanocidal activity},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {2},
pages = {75--90},
year = {2023},
url = {https://doi.org/10.1007/s10822-022-00491-0},
doi = {10.1007/S10822-022-00491-0},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LlanosARSMPFCSGT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MaSLRWLN23,
author = {Huaiqin Ma and
Qingwen Shi and
Xuhua Li and
Junli Ren and
Yuhan Wang and
Zhijian Li and
Lulu Ning},
title = {Molecular and thermodynamic insights into interfacial interactions
between collagen and cellulose investigated by molecular dynamics
simulation and umbrella sampling},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {1},
pages = {39--51},
year = {2023},
url = {https://doi.org/10.1007/s10822-022-00489-8},
doi = {10.1007/S10822-022-00489-8},
timestamp = {Tue, 31 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/MaSLRWLN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MeyenburgDBR23,
author = {Christian Meyenburg and
Uschi Dolfus and
Hans Briem and
Matthias Rarey},
title = {Galileo: Three-dimensional searching in large combinatorial fragment
spaces on the example of pharmacophores},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {1},
pages = {1--16},
year = {2023},
url = {https://doi.org/10.1007/s10822-022-00485-y},
doi = {10.1007/S10822-022-00485-Y},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/MeyenburgDBR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MonariGC23,
author = {Luca Monari and
Katia Galentino and
Marco Cecchini},
title = {ChemFlow{\_}py: a flexible toolkit for docking and rescoring},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {11},
pages = {565--572},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00527-z},
doi = {10.1007/S10822-023-00527-Z},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MonariGC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MoritaSH23,
author = {Rikuri Morita and
Yasuteru Shigeta and
Ryuhei Harada},
title = {Efficient screening of protein-ligand complexes in lipid bilayers
using LoCoMock score},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {4},
pages = {217--225},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00502-8},
doi = {10.1007/S10822-023-00502-8},
timestamp = {Wed, 12 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MoritaSH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PaciottiMCR23,
author = {Roberto Paciotti and
Alessandro Marrone and
Cecilia Coletti and
Nazzareno Re},
title = {Improving the accuracy of the {FMO} binding affinity prediction of
ligand-receptor complexes containing metals},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {707--719},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00532-2},
doi = {10.1007/S10822-023-00532-2},
timestamp = {Wed, 08 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/PaciottiMCR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParkK23,
author = {Gyoung Jin Park and
Nam Sook Kang},
title = {ADis-QSAR: a machine learning model based on biological activity differences
of compounds},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {9},
pages = {435--451},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00517-1},
doi = {10.1007/S10822-023-00517-1},
timestamp = {Fri, 04 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ParkK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PereiraAOGSA23,
author = {Tiago O. Pereira and
Maryam Abbasi and
Rita I. Oliveira and
Romina A. Guedes and
Jorge A. R. Salvador and
Joel P. Arrais},
title = {Artificial intelligence for prediction of biological activities and
generation of molecular hits using stereochemical information},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {791--806},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00539-9},
doi = {10.1007/S10822-023-00539-9},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PereiraAOGSA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PomariciWQBGFL23,
author = {Nancy D. Pomarici and
Franz Waibl and
Patrick K. Quoika and
Alexander Bujotzek and
Guy Georges and
Monica L. Fern{\'{a}}ndez{-}Quintero and
Klaus R. Liedl},
title = {Structural mechanism of Fab domain dissociation as a measure of interface
stability},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {4},
pages = {201--215},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00501-9},
doi = {10.1007/S10822-023-00501-9},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PomariciWQBGFL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RambaherZGGF23,
author = {Martina Hrast Rambaher and
Irena Zdovc and
Nina Kocevar Glavac and
Stanislav Gobec and
Rok Frlan},
title = {Mur ligase {F} as a new target for the flavonoids quercitrin, myricetin,
and (-)-epicatechin},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {721--733},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00535-z},
doi = {10.1007/S10822-023-00535-Z},
timestamp = {Thu, 09 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/RambaherZGGF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RemingtonMBFSL23,
author = {Jacob M. Remington and
Kyle T. McKay and
Noah B. Beckage and
Jonathon B. Ferrell and
Severin T. Schneebeli and
Jianing Li},
title = {GPCRLigNet: rapid screening for {GPCR} active ligands using machine
learning},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {3},
pages = {147--156},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00497-2},
doi = {10.1007/S10822-023-00497-2},
timestamp = {Thu, 09 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/RemingtonMBFSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RenVLOJ23,
author = {Jinhong Ren and
Tasneem M. Vaid and
Hyun Lee and
Isabel Ojeda and
Michael E. Johnson},
title = {Evaluation of interactions between the hepatitis {C} virus {NS3/4A}
and sulfonamidobenzamide based molecules using molecular docking,
molecular dynamics simulations and binding free energy calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {1},
pages = {53--65},
year = {2023},
url = {https://doi.org/10.1007/s10822-022-00490-1},
doi = {10.1007/S10822-022-00490-1},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/RenVLOJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ReynaLunaSVF23,
author = {Julieta Reyna{-}Luna and
Luis Soriano{-}Agueda and
Christiaan Jardinez Vera and
Marco Franco{-}P{\'{e}}rez},
title = {Insights into the coordination chemistry of antineoplastic doxorubicin
with 3d-transition metal ions Zn\({}^{\mbox{2+}}\), Cu\({}^{\mbox{2+}}\),
and VO\({}^{\mbox{2+}}\): a study using well-calibrated thermodynamic
cycles and chemical interaction quantum chemistry models},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {7},
pages = {279--299},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00506-4},
doi = {10.1007/S10822-023-00506-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ReynaLunaSVF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ShahrakiSK23,
author = {Aida Shahraki and
Jana Selent and
Peter Kolb},
title = {On the construction of {LIECE} models for the serotonin receptor 5-HT\({}_{\mbox{
2A}}\)R},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {7},
pages = {313--323},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00507-3},
doi = {10.1007/S10822-023-00507-3},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ShahrakiSK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SilvaF23,
author = {Wemenes Jos{\'{e}} Lima Silva and
Renato Ferreira de Freitas},
title = {Assessing the performance of docking, FEP, and {MM/GBSA} methods on
a series of {KLK6} inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {9},
pages = {407--418},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00515-3},
doi = {10.1007/S10822-023-00515-3},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SilvaF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SilvaF23a,
author = {Wemenes Jos{\'{e}} Lima Silva and
Renato Ferreira de Freitas},
title = {Correction to: Assessing the performance of docking, FEP, and {MM/GBSA}
methods on a series of {KLK6} inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {10},
pages = {505},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00521-5},
doi = {10.1007/S10822-023-00521-5},
timestamp = {Fri, 25 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SilvaF23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SinghSS23,
author = {Jaikee Kumar Singh and
Jai Singh and
Sandeep Kumar Srivastava},
title = {Investigating the role of glycans in Omicron sub-lineages {XBB.1.5}
and {XBB.1.16} binding to host receptor using molecular dynamics and
binding free energy calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {11},
pages = {551--563},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00526-0},
doi = {10.1007/S10822-023-00526-0},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SinghSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SosninaSF23,
author = {Ekaterina A. Sosnina and
Sergey Sosnin and
Maxim V. Fedorov},
title = {Improvement of multi-task learning by data enrichment: application
for drug discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {4},
pages = {183--200},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00500-w},
doi = {10.1007/S10822-023-00500-W},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SosninaSF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SouzaSG23,
author = {Anacleto Silva de Souza and
Robson Francisco de Souza and
Cristiane Rodrigues Guzzo},
title = {Cooperative and structural relationships of the trimeric Spike with
infectivity and antibody escape of the strains Delta {(B.1.617.2)}
and Omicron (BA.2, BA.5, and {BQ.1)}},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {585--606},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00534-0},
doi = {10.1007/S10822-023-00534-0},
timestamp = {Wed, 08 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SouzaSG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/StampolakiSZK23,
author = {Marianna Stampolaki and
Ioannis Stylianakis and
Helen I. Zgurskaya and
Antonios Kolocouris},
title = {Study of {SQ109} analogs binding to mycobacterium MmpL3 transporter
using {MD} simulations and alchemical relative binding free energy
calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {5},
pages = {245--264},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00504-6},
doi = {10.1007/S10822-023-00504-6},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/StampolakiSZK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/StroetCEWKDEVHMBGLSGMK23,
author = {Martin Stroet and
Bertrand Caron and
Martin S. Engler and
Jimi van der Woning and
Aude Kauffmann and
Marc van Dijk and
Mohammed El{-}Kebir and
Koen Visscher and
Josef Holownia and
Callum Macfarlane and
Brian J. Bennion and
Svetlana Gelpi{-}Dominguez and
Felice C. Lightstone and
Tijs van der Storm and
Daan P. Geerke and
Alan E. Mark and
Gunnar W. Klau},
title = {OFraMP: a fragment-based tool to facilitate the parametrization of
large molecules},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {8},
pages = {357--371},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00511-7},
doi = {10.1007/S10822-023-00511-7},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/StroetCEWKDEVHMBGLSGMK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/StylianakisZLPK23,
author = {Ioannis Stylianakis and
Nikolaos Zervos and
Jenn{-}Huei Lii and
Dimitrios A. Pantazis and
Antonios Kolocouris},
title = {Conformational energies of reference organic molecules: benchmarking
of common efficient computational methods against coupled cluster
theory},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {607--656},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00513-5},
doi = {10.1007/S10822-023-00513-5},
timestamp = {Thu, 09 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/StylianakisZLPK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/StylianakisZLPK23a,
author = {Ioannis Stylianakis and
Nikolaos Zervos and
Jenn{-}Huei Lii and
Dimitrios A. Pantazis and
Antonios Kolocouris},
title = {Correction to: Conformational energies of reference organic molecules:
benchmarking of common efficient computational methods against coupled
cluster theory},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {657},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00531-3},
doi = {10.1007/S10822-023-00531-3},
timestamp = {Wed, 08 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/StylianakisZLPK23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TaylorH23,
author = {Mackenzie Taylor and
Junming Ho},
title = {{MM/GBSA} prediction of relative binding affinities of carbonic anhydrase
inhibitors: effect of atomic charges and comparison with Autodock4\({}_{\mbox{Zn}}\)},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {4},
pages = {167--182},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00499-0},
doi = {10.1007/S10822-023-00499-0},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TaylorH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/UmederaYCKNB23,
author = {Kohei Umedera and
Atsushi Yoshimori and
Hengwei Chen and
Hiroyuki Kouji and
Hiroyuki Nakamura and
J{\"{u}}rgen Bajorath},
title = {DeepCubist: Molecular Generator for Designing Peptidomimetics based
on Complex three-dimensional scaffolds},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {2},
pages = {107--115},
year = {2023},
url = {https://doi.org/10.1007/s10822-022-00493-y},
doi = {10.1007/S10822-022-00493-Y},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/UmederaYCKNB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VarikotiSKKBZK23,
author = {Rohith Anand Varikoti and
Katherine J. Schultz and
Chathuri J. Kombala and
Agustin Kruel and
Kristoffer R. Brandvold and
Mowei Zhou and
Neeraj Kumar},
title = {Integrated data-driven and experimental approaches to accelerate lead
optimization targeting SARS-CoV-2 main protease},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {8},
pages = {339--355},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00509-1},
doi = {10.1007/S10822-023-00509-1},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VarikotiSKKBZK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VerissimoPFGKHM23,
author = {Gabriel Corr{\^{e}}a Ver{\'{\i}}ssimo and
Simone Queiroz Pantale{\~{a}}o and
Philipe de Oliveira Fernandes and
Jadson Castro Gertrudes and
Thales Kronenberger and
K{\'{a}}thia Maria Hon{\'{o}}rio and
Vinicius Gon{\c{c}}alves Maltarollo},
title = {{MASSA} Algorithm: an automated rational sampling of training and
test subsets for {QSAR} modeling},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {735--754},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00536-y},
doi = {10.1007/S10822-023-00536-Y},
timestamp = {Mon, 06 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VerissimoPFGKHM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VinuthaR23,
author = {A. S. Vinutha and
Rajasekaran Ramalingam},
title = {Insight on the mechanism of hexameric Pseudin-4 against bacterial
membrane-mimetic environment},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {9},
pages = {419--434},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00516-2},
doi = {10.1007/S10822-023-00516-2},
timestamp = {Fri, 04 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VinuthaR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/XiongWWLPWWGB23,
author = {Youjin Xiong and
Yiqing Wang and
Yisheng Wang and
Chenmei Li and
Yusong Peng and
Junyu Wu and
Lingyun Gu and
Christopher J. Butch},
title = {Improving drug discovery with a hybrid deep generative model using
reinforcement learning trained on a Bayesian docking approximation},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {11},
pages = {507--517},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00523-3},
doi = {10.1007/S10822-023-00523-3},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/XiongWWLPWWGB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Xu23,
author = {Huafeng Xu},
title = {The slow but steady rise of binding free energy calculations in drug
discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {2},
pages = {67--74},
year = {2023},
url = {https://doi.org/10.1007/s10822-022-00494-x},
doi = {10.1007/S10822-022-00494-X},
timestamp = {Tue, 31 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Xu23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhangCCQWLZ23,
author = {Yijing Zhang and
Shiyao Chen and
Taeyoung Choi and
Yuzheng Qi and
Qianhui Wang and
Guanyi Li and
Yaxue Zhao},
title = {Molecular dynamics simulations reveal the inhibition mechanism of
Cdc42 by RhoGDI1},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {7},
pages = {301--312},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00508-2},
doi = {10.1007/S10822-023-00508-2},
timestamp = {Tue, 27 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZhangCCQWLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhangHZYHTL23,
author = {Qianqian Zhang and
Jianting Han and
Yongchang Zhu and
Fansen Yu and
Xiaopeng Hu and
Henry H. Y. Tong and
Huanxiang Liu},
title = {Discovery of novel and potent InhA direct inhibitors by ensemble docking-based
virtual screening and biological assays},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {12},
pages = {695--706},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00530-4},
doi = {10.1007/S10822-023-00530-4},
timestamp = {Wed, 08 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ZhangHZYHTL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhangL23,
author = {Lu Zhang and
Haiyan Liu},
title = {Exploring binding positions and backbone conformations of peptide
ligands of proteins with a backbone-centred statistical energy function},
journal = {J. Comput. Aided Mol. Des.},
volume = {37},
number = {10},
pages = {463--478},
year = {2023},
url = {https://doi.org/10.1007/s10822-023-00518-0},
doi = {10.1007/S10822-023-00518-0},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ZhangL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AbdoP22,
author = {Ammar Abdo and
Maude Pupin},
title = {Turbo prediction: a new approach for bioactivity prediction},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {1},
pages = {77--85},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00440-3},
doi = {10.1007/S10822-021-00440-3},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AbdoP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AgostaKC22,
author = {Federica Agosta and
Glen E. Kellogg and
Pietro Cozzini},
title = {From oncoproteins to spike proteins: the evaluation of intramolecular
stability using hydropathic force field},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {11},
pages = {797--804},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00477-y},
doi = {10.1007/S10822-022-00477-Y},
timestamp = {Fri, 11 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AgostaKC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AliagasGLS22,
author = {Ignacio Aliagas and
Alberto Gobbi and
Man{-}Ling Lee and
Benjamin D. Sellers},
title = {Comparison of logP and logD correction models trained with public
and proprietary data sets},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {3},
pages = {253--262},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00450-9},
doi = {10.1007/S10822-022-00450-9},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AliagasGLS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AmezcuaSGM22,
author = {Martin Amezcua and
Jeffry Setiadi and
Yunhui Ge and
David L. Mobley},
title = {An overview of the {SAMPL8} host-guest binding challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {10},
pages = {707--734},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00462-5},
doi = {10.1007/S10822-022-00462-5},
timestamp = {Sun, 13 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AmezcuaSGM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AzimiWKKDG22,
author = {Solmaz Azimi and
Joe Z. Wu and
Sheenam Khuttan and
Tom Kurtzman and
Nanjie Deng and
Emilio Gallicchio},
title = {Application of the alchemical transfer and potential of mean force
methods to the {SAMPL8} host-guest blinded challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {1},
pages = {63--76},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00437-y},
doi = {10.1007/S10822-021-00437-Y},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AzimiWKKDG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BlaschkeB22,
author = {Thomas Blaschke and
J{\"{u}}rgen Bajorath},
title = {Fine-tuning of a generative neural network for designing multi-target
compounds},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {5},
pages = {363--371},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00392-8},
doi = {10.1007/S10822-021-00392-8},
timestamp = {Thu, 25 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BlaschkeB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CharoenkwanCSLM22,
author = {Phasit Charoenkwan and
Pramote Chumnanpuen and
Nalini Schaduangrat and
Pietro Lio' and
Mohammad Ali Moni and
Watshara Shoombuatong},
title = {Improved prediction and characterization of blood-brain barrier penetrating
peptides using estimated propensity scores of dipeptides},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {11},
pages = {781--796},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00476-z},
doi = {10.1007/S10822-022-00476-Z},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/CharoenkwanCSLM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChiACBM22,
author = {Luz Am{\'{e}}rica Chi and
Somayeh Asgharpour and
Jos{\'{e}} Correa{-}Basurto and
Cindy Rodr{\'{\i}}guez Bandala and
Marlet Mart{\'{\i}}nez{-}Archundia},
title = {Unveiling the {G4-PAMAM} capacity to bind and protect Ang-(1-7) bioactive
peptide by molecular dynamics simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {9},
pages = {653--675},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00470-5},
doi = {10.1007/S10822-022-00470-5},
timestamp = {Wed, 04 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChiACBM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CuiZW022,
author = {Mengqi Cui and
Kun Zhang and
Ruihan Wu and
Juan Du},
title = {Exploring the interaction mechanism between antagonist and the jasmonate
receptor complex by molecular dynamics simulation},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {2},
pages = {141--155},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00441-w},
doi = {10.1007/S10822-022-00441-W},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CuiZW022.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DelaunayH22,
author = {Maxence Delaunay and
T{\^{a}}p Ha{-}Duong},
title = {Des3PI: a fragment-based approach to design cyclic peptides targeting
protein-protein interactions},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {8},
pages = {605--621},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00468-z},
doi = {10.1007/S10822-022-00468-Z},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DelaunayH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Drie22,
author = {John H. Van Drie},
title = {Hit diffusion: limitations to drug discovery and structure-based design},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {5},
pages = {373--379},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00425-2},
doi = {10.1007/S10822-021-00425-2},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Drie22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Durrant22,
author = {Jacob D. Durrant},
title = {Prot2Prot: a deep learning model for rapid, photorealistic macromolecular
visualization},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {9},
pages = {677--686},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00471-4},
doi = {10.1007/S10822-022-00471-4},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Durrant22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DuttaDSL22,
author = {Nivedita Dutta and
Indrajit Deb and
Joanna Sarzynska and
Ansuman Lahiri},
title = {Data-informed reparameterization of modified {RNA} and the effect
of explicit water models: application to pseudouridine and derivatives},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {3},
pages = {205--224},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00447-4},
doi = {10.1007/S10822-022-00447-4},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DuttaDSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GanKCTJAL22,
author = {Jessie Low Gan and
Dhruv Kumar and
Cynthia Chen and
Bryn C. Taylor and
Benjamin R. Jagger and
Rommie E. Amaro and
Christopher T. Lee},
title = {Benchmarking ensemble docking methods in {D3R} Grand Challenge 4},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {2},
pages = {87--99},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00433-2},
doi = {10.1007/S10822-021-00433-2},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GanKCTJAL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Garcia-MarinRV22,
author = {Javier Garc{\'{\i}}a{-}Mar{\'{\i}}n and
Diego Rodr{\'{e}}guez{-}Puyol and
Juan Jos{\'{e}} Vaquero},
title = {Insight into the mechanism of molecular recognition between human
Integrin-Linked Kinase and Cpd22 and its implication at atomic level},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {8},
pages = {575--589},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00466-1},
doi = {10.1007/S10822-022-00466-1},
timestamp = {Tue, 06 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Garcia-MarinRV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GeMDEM22,
author = {Yunhui Ge and
Oliver J. Melling and
Weiming Dong and
Jonathan W. Essex and
David L. Mobley},
title = {Enhancing sampling of water rehydration upon ligand binding using
variants of grand canonical Monte Carlo},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {10},
pages = {767--779},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00479-w},
doi = {10.1007/S10822-022-00479-W},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GeMDEM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Goller22,
author = {Andreas H. G{\"{o}}ller},
title = {Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds
and the issue of continuum solvation},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {11},
pages = {805--824},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00480-3},
doi = {10.1007/S10822-022-00480-3},
timestamp = {Fri, 11 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Goller22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GrosjeanIAMCDB22,
author = {Harold Grosjean and
Mehtap Isik and
Anthony Aimon and
David L. Mobley and
John D. Chodera and
Frank von Delft and
Philip C. Biggin},
title = {{SAMPL7} protein-ligand challenge: {A} community-wide evaluation of
computational methods against fragment screening and pose-prediction},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {4},
pages = {291--311},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00452-7},
doi = {10.1007/S10822-022-00452-7},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GrosjeanIAMCDB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HsuRSTS22,
author = {Wei{-}Tse Hsu and
Dominique A. Ramirez and
Tarek Sammakia and
Zhongping Tan and
Michael R. Shirts},
title = {Identifying signatures of proteolytic stability and monomeric propensity
in O-glycosylated insulin using molecular simulation},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {4},
pages = {313--328},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00453-6},
doi = {10.1007/S10822-022-00453-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HsuRSTS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HudsonAMWPPJWB22,
author = {Phillip S. Hudson and
F{\'{e}}lix Aviat and
Rub{\'{e}}n Meana{-}Pa{\~{n}}eda and
Luke C. Warrensford and
Benjamin C. Pollard and
Samarjeet Prasad and
Michael R. Jones and
H. Lee Woodcock III and
Bernard R. Brooks},
title = {Obtaining {QM/MM} binding free energies in the {SAMPL8} drugs of abuse
challenge: indirect approaches},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {4},
pages = {263--277},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00443-8},
doi = {10.1007/S10822-022-00443-8},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HudsonAMWPPJWB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KumarBSSK22,
author = {Sandeep Kumar and
Rajendra Bhadane and
Shruti Shandilya and
Outi M. H. Salo{-}Ahen and
Suman Kapila},
title = {Identification of HPr kinase/phosphorylase inhibitors: novel antimicrobials
against resistant Enterococcus faecalis},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {7},
pages = {507--520},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00461-6},
doi = {10.1007/S10822-022-00461-6},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KumarBSSK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Lajiness22,
author = {Michael S. Lajiness},
title = {The power of a mentor},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {5},
pages = {339--340},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00398-2},
doi = {10.1007/S10822-021-00398-2},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Lajiness22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LanevskijDS22,
author = {Kiril Lanevskij and
Remigijus Didziapetris and
Andrius Sazonovas},
title = {Physicochemical {QSAR} analysis of hERG inhibition revisited: towards
a quantitative potency prediction},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {12},
pages = {837--849},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00483-0},
doi = {10.1007/S10822-022-00483-0},
timestamp = {Mon, 05 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LanevskijDS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiLSP22,
author = {Jinxing Li and
Chao Li and
Jun Sun and
Vasile Palade},
title = {RDPSOVina: the random drift particle swarm optimization for protein-ligand
docking},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {6},
pages = {415--425},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00455-4},
doi = {10.1007/S10822-022-00455-4},
timestamp = {Sat, 10 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiLSP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LimLYK22,
author = {Sangrak Lim and
Yong Oh Lee and
Juyong Yoon and
Young Jun Kim},
title = {Affinity prediction using deep learning based on {SMILES} input for
{D3R} grand challenge 4},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {3},
pages = {225--235},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00448-3},
doi = {10.1007/S10822-022-00448-3},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LimLYK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuLRW22,
author = {Ruifeng Liu and
Srinivas Laxminarayan and
Jaques Reifman and
Anders Wallqvist},
title = {Enabling data-limited chemical bioactivity predictions through deep
neural network transfer learning},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {12},
pages = {867--878},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00486-x},
doi = {10.1007/S10822-022-00486-X},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiuLRW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuZCGYZLS22,
author = {Xiao Liu and
Lei Zheng and
Yalong Cong and
Zhihao Gong and
Zhixiang Yin and
John Z. H. Zhang and
Zhirong Liu and
Zhaoxi Sun},
title = {Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene
host-guest binding: {II.} regression and dielectric constant},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {12},
pages = {879--894},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00487-w},
doi = {10.1007/S10822-022-00487-W},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiuZCGYZLS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuZQZS22,
author = {Xiao Liu and
Lei Zheng and
Chu Qin and
John Z. H. Zhang and
Zhaoxi Sun},
title = {Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene
host-guest binding: I. Standard procedure},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {10},
pages = {735--752},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00475-0},
doi = {10.1007/S10822-022-00475-0},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LiuZQZS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MaedaSTM22,
author = {Itsuki Maeda and
Akinori Sato and
Shunsuke Tamura and
Tomoyuki Miyao},
title = {Ligand-based approaches to activity prediction for the early stage
of structure-activity-relationship progression},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {3},
pages = {237--252},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00449-2},
doi = {10.1007/S10822-022-00449-2},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MaedaSTM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Maggiora22,
author = {Gerry Maggiora},
title = {Is the reductionist paradox an Achilles Heel of drug discovery?},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {5},
pages = {329--338},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00457-2},
doi = {10.1007/S10822-022-00457-2},
timestamp = {Wed, 03 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Maggiora22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MalikL22,
author = {Faisal Malik and
Zhijun Li},
title = {Is there a common allosteric binding site for G-protein coupled receptors?},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {6},
pages = {405--413},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00454-5},
doi = {10.1007/S10822-022-00454-5},
timestamp = {Sat, 10 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MalikL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MarkthalerKH22,
author = {Daniel Markthaler and
Hamzeh Kraus and
Niels Hansen},
title = {Binding free energies for the {SAMPL8} {CB8} "Drugs of Abuse" challenge
from umbrella sampling combined with Hamiltonian replica exchange},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {1},
pages = {1--9},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00439-w},
doi = {10.1007/S10822-021-00439-W},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MarkthalerKH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Medina-FrancoSL22,
author = {Jos{\'{e}} L. Medina{-}Franco and
Norberto S{\'{a}}nchez{-}Cruz and
Edgar L{\'{o}}pez{-}L{\'{o}}pez and
B{\'{a}}rbara I. D{\'{\i}}az{-}Eufracio},
title = {Progress on open chemoinformatic tools for expanding and exploring
the chemical space},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {5},
pages = {341--354},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00399-1},
doi = {10.1007/S10822-021-00399-1},
timestamp = {Thu, 25 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Medina-FrancoSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MeeluaOJ22,
author = {Wijitra Meelua and
Julianna Ol{\'{a}}h and
Jitrayut Jitonnom},
title = {Role of water coordination at zinc binding site and its catalytic
pathway of dizinc creatininase: insights from quantum cluster approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {4},
pages = {279--289},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00451-8},
doi = {10.1007/S10822-022-00451-8},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MeeluaOJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MoraSM22,
author = {Andr{\'{e}}s Mart{\'{\i}}nez Mora and
Vigneshwari Subramanian and
Filip Miljkovic},
title = {Multi-task convolutional neural networks for predicting in vitro clearance
endpoints from molecular images},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {6},
pages = {443--457},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00458-1},
doi = {10.1007/S10822-022-00458-1},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MoraSM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MousaHT22,
author = {Lubabah A. Mousa and
M{\'{a}}mon M. Hatmal and
Mutasem O. Taha},
title = {Exploiting activity cliffs for building pharmacophore models and comparison
with other pharmacophore generation methods: sphingosine kinase 1
as case study},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {1},
pages = {39--62},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00435-0},
doi = {10.1007/S10822-021-00435-0},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/MousaHT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NagarajanSVJ22,
author = {Hemavathy Nagarajan and
Ansar Samdani and
Umashankar Vetrivel and
Jeyaraman Jeyakanthan},
title = {Deciphering the conformational transitions of {LIMK2} active and inactive
states to ponder specific druggable states through microsecond scale
molecular dynamics simulation},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {6},
pages = {459--482},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00459-0},
doi = {10.1007/S10822-022-00459-0},
timestamp = {Fri, 02 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NagarajanSVJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OchoaCF22,
author = {Rodrigo Ochoa and
Pilar Cossio and
Thomas Fox},
title = {Protocol for iterative optimization of modified peptides bound to
protein targets},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {11},
pages = {825--835},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00482-1},
doi = {10.1007/S10822-022-00482-1},
timestamp = {Fri, 11 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/OchoaCF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PaciottiCMR22,
author = {Roberto Paciotti and
Cecilia Coletti and
Alessandro Marrone and
Nazzareno Re},
title = {The {FMO2} analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA
G-Quadruplex case study},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {12},
pages = {851--866},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00484-z},
doi = {10.1007/S10822-022-00484-Z},
timestamp = {Thu, 01 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/PaciottiCMR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PennerMBFGTMR22,
author = {Patrick Penner and
Virginie Y. Martiny and
Louis Bellmann and
Florian Flachsenberg and
Marcus Gastreich and
Isabelle Theret and
Christophe Meyer and
Matthias Rarey},
title = {FastGrow: on-the-fly growing and its application to {DYRK1A}},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {9},
pages = {639--651},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00469-y},
doi = {10.1007/S10822-022-00469-Y},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PennerMBFGTMR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ProiaRASMCR22,
author = {Eleonora Proia and
Alessio Ragno and
Lorenzo Antonini and
Manuela Sabatino and
Milan Mladenovic and
Roberto Capobianco and
Rino Ragno},
title = {Ligand-based and structure-based studies to develop predictive models
for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {7},
pages = {483--505},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00460-7},
doi = {10.1007/S10822-022-00460-7},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ProiaRASMCR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RaczDBKMH22,
author = {Anita R{\'{a}}cz and
Timothy B. Dunn and
D{\'{a}}vid Bajusz and
Taewon David Kim and
Ram{\'{o}}n Alain Miranda{-}Quintana and
K{\'{a}}roly H{\'{e}}berger},
title = {Extended continuous similarity indices: theory and application for
{QSAR} descriptor selection},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {3},
pages = {157--173},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00444-7},
doi = {10.1007/S10822-022-00444-7},
timestamp = {Fri, 03 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RaczDBKMH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RibonePAV22,
author = {Sergio R. Ribone and
S. Alexis Paz and
Cameron F. Abrams and
Marcos A. Villarreal},
title = {Target identification for repurposed drugs active against SARS-CoV-2
via high-throughput inverse docking},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {1},
pages = {25--37},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00432-3},
doi = {10.1007/S10822-021-00432-3},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/RibonePAV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RienzoFRFM22,
author = {Lorenzo Di Rienzo and
Luca De Flaviis and
Giancarlo Ruocco and
Viola Folli and
Edoardo Milanetti},
title = {Binding site identification of {G} protein-coupled receptors through
a 3D Zernike polynomials-based method: application to C. elegans olfactory
receptors},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {1},
pages = {11--24},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00434-1},
doi = {10.1007/S10822-021-00434-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RienzoFRFM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RiesNWRBCKR22,
author = {Benjamin Ries and
Karl Normak and
R. Gregor Wei{\ss} and
Salom{\'{e}} Rieder and
Em{\'{\i}}lia P. Barros and
Candide Champion and
Gerhard K{\"{o}}nig and
Sereina Riniker},
title = {Relative free-energy calculations for scaffold hopping-type transformations
with an automated {RE-EDS} sampling procedure},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {2},
pages = {117--130},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00436-z},
doi = {10.1007/S10822-021-00436-Z},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RiesNWRBCKR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RiesRRHR22,
author = {Benjamin Ries and
Salom{\'{e}} Rieder and
Clemens Rhiner and
Philippe H. H{\"{u}}nenberger and
Sereina Riniker},
title = {RestraintMaker: a graph-based approach to select distance restraints
in free-energy calculations with dual topology},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {3},
pages = {175--192},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00445-6},
doi = {10.1007/S10822-022-00445-6},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RiesRRHR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Rodriguez-Perez22,
author = {Raquel Rodr{\'{\i}}guez{-}P{\'{e}}rez and
J{\"{u}}rgen Bajorath},
title = {Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics
and Drug Discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {5},
pages = {355--362},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00442-9},
doi = {10.1007/S10822-022-00442-9},
timestamp = {Thu, 25 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Rodriguez-Perez22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RodriguezTSP22,
author = {Sergio A. Rodriguez and
Jasmine Vy Tran and
Spencer J. Sabatino and
Andrew S. Paluch},
title = {Predicting octanol/water partition coefficients and pKa for the {SAMPL7}
challenge using the SM12, {SM8} and {SMD} solvation models},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {9},
pages = {687--705},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00474-1},
doi = {10.1007/S10822-022-00474-1},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/RodriguezTSP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RoyB22,
author = {Parthajit Roy and
Dhananjay Bhattacharyya},
title = {Contact networks in {RNA:} a structural bioinformatics study with
a new tool},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {2},
pages = {131--140},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00438-x},
doi = {10.1007/S10822-021-00438-X},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RoyB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Sainz-DiazLBFS22,
author = {C. Ignacio Sainz{-}D{\'{\i}}az and
Alexander P{\'{e}}rez de la Luz and
Carolina Barrientos{-}Salcedo and
Misaela Francisco{-}Marquez and
Catalina Soriano{-}Correa},
title = {Crystal polymorphism and spectroscopical properties of sulfonamides
in solid state by means of First Principles calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {7},
pages = {549--562},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00465-2},
doi = {10.1007/S10822-022-00465-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Sainz-DiazLBFS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Shanmugasundaram22,
author = {Veerabahu Shanmugasundaram and
J{\"{u}}rgen Bajorath and
Ralph E. Christoffersen and
James D. Petke and
W. Jeffrey Howe and
Mark A. Johnson and
Dimitris K. Agrafiotis and
Pil Lee and
Leslie A. Kuhn and
Jay T. Goodwin and
M. Katharine Holloway and
Thompson N. Doman and
W. Patrick Walters and
Suzanne K. Schreyer and
Jos{\'{e}} L. Medina{-}Franco and
Karina Mart{\'{\i}}nez{-}Mayorga and
Linda L. Restifo},
title = {Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary
mentor, colleague, collaborator, and innovator},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {9},
pages = {623--638},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00473-2},
doi = {10.1007/S10822-022-00473-2},
timestamp = {Mon, 05 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Shanmugasundaram22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SunBVCFOCKSDL22,
author = {Qinfang Sun and
Avik Biswas and
R. S. K. Vijayan and
Pierrick Craveur and
Stefano Forli and
Arthur J. Olson and
Andres Emanuelli Castaner and
Karen Kirby and
Stefan G. Sarafianos and
Nan{-}Jie Deng and
Ronald M. Levy},
title = {Structure-based virtual screening workflow to identify antivirals
targeting {HIV-1} capsid},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {3},
pages = {193--203},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00446-5},
doi = {10.1007/S10822-022-00446-5},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SunBVCFOCKSDL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TosstorffRCRKSN22,
author = {Andreas Tosstorff and
Markus G. Rudolph and
Jason C. Cole and
Michael Reutlinger and
Christian Kramer and
Herv{\'{e}} Schaffhauser and
Agn{\`{e}}s Nilly and
Alexander Flohr and
Bernd Kuhn},
title = {A high quality, industrial data set for binding affinity prediction:
performance comparison in different early drug discovery scenarios},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {10},
pages = {753--765},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00478-x},
doi = {10.1007/S10822-022-00478-X},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TosstorffRCRKSN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VermaHSS22,
author = {Jyoti Verma and
Abdul Hasan and
Sujatha Sunil and
Naidu Subbarao},
title = {In silico identification and in vitro antiviral validation of potential
inhibitors against Chikungunya virus},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {7},
pages = {521--536},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00463-4},
doi = {10.1007/S10822-022-00463-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VermaHSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WaiblKFLL22,
author = {Franz Waibl and
Johannes Kraml and
Monica L. Fern{\'{a}}ndez{-}Quintero and
Johannes R. Loeffler and
Klaus R. Liedl},
title = {Explicit solvation thermodynamics in ionic solution: extending grid
inhomogeneous solvation theory to solvation free energy of salt-water
mixtures},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {2},
pages = {101--116},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00429-y},
doi = {10.1007/S10822-021-00429-Y},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WaiblKFLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Walters22,
author = {W. Patrick Walters},
title = {Comparing classification models - a practical tutorial},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {5},
pages = {381--389},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00417-2},
doi = {10.1007/S10822-021-00417-2},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Walters22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WeberMBPKZC22,
author = {Jeffrey K. Weber and
Joseph A. Morrone and
Sugato Bagchi and
Jan D. Estrada Pabon and
Seung{-}gu Kang and
Leili Zhang and
Wendy D. Cornell},
title = {Simplified, interpretable graph convolutional neural networks for
small molecule activity prediction},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {5},
pages = {391--404},
year = {2022},
url = {https://doi.org/10.1007/s10822-021-00421-6},
doi = {10.1007/S10822-021-00421-6},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WeberMBPKZC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WuB22,
author = {Yujin Wu and
Charles L. Brooks III},
title = {Covalent docking in {CDOCKER}},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {8},
pages = {563--574},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00472-3},
doi = {10.1007/S10822-022-00472-3},
timestamp = {Thu, 06 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WuB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WuHXOLHC22,
author = {Qiyang Wu and
Tianyang Huang and
Songyan Xia and
Frank Otto and
Tzong{-}Yi Lee and
Hsien{-}Da Huang and
Ying{-}Chih Chiang},
title = {On the force field optimisation of {\(\beta\)}-lactam cores using
the force field Toolkit},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {7},
pages = {537--547},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00464-3},
doi = {10.1007/S10822-022-00464-3},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WuHXOLHC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YauL22,
author = {Mei Qian Yau and
Jason S. E. Loo},
title = {Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering
the role of {MM/GBSA}},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {6},
pages = {427--441},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00456-3},
doi = {10.1007/S10822-022-00456-3},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/YauL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhuLWMLL22,
author = {Kai Zhu and
Cui Li and
Kingsley Y. Wu and
Christopher Mohr and
Xun Li and
Brian Lanman},
title = {Modeling receptor flexibility in the structure-based design of KRAS\({}^{\mbox{G12C}}\)
inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {8},
pages = {591--604},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00467-0},
doi = {10.1007/S10822-022-00467-0},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZhuLWMLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AbdoP21,
author = {Ammar Abdo and
Maude Pupin},
title = {{LINGO-DL:} a text-based approach for molecular similarity searching},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {5},
pages = {657--665},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00383-9},
doi = {10.1007/S10822-021-00383-9},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AbdoP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AgamennoneSMP21,
author = {Mariangela Agamennone and
Loriano Storchi and
Alessandro Marrone and
Roberto Paciotti},
title = {Hampering the early aggregation of PrP-E200K protein by charge-based
inhibitors: a computational study},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {6},
pages = {751--770},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00393-7},
doi = {10.1007/S10822-021-00393-7},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AgamennoneSMP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AliCKVH21,
author = {Hafiz Saqib Ali and
Arghya Chakravorty and
Jas Kalayan and
Sam P. de Visser and
Richard H. Henchman},
title = {Energy-entropy method using multiscale cell correlation to calculate
binding free energies in the {SAMPL8} host-guest challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {8},
pages = {911--921},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00406-5},
doi = {10.1007/S10822-021-00406-5},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AliCKVH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AmezcuaEM21,
author = {Martin Amezcua and
Lea El{-}Khoury and
David L. Mobley},
title = {{SAMPL7} Host-Guest Challenge Overview: assessing the reliability
of polarizable and non-polarizable methods for binding free energy
calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {1},
pages = {1--35},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00363-5},
doi = {10.1007/S10822-020-00363-5},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AmezcuaEM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BahrNKNVICM21,
author = {Matthew N. Bahr and
Aakankschit Nandkeolyar and
John K. Kenna and
Neysa Nevins and
Luigi Da Vi{\`{a}} and
Mehtap Isik and
John D. Chodera and
David L. Mobley},
title = {Automated high throughput pK\({}_{\mbox{a}}\) and distribution coefficient
measurements of pharmaceutical compounds for the {SAMPL8} blind prediction
challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {11},
pages = {1141--1155},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00427-0},
doi = {10.1007/S10822-021-00427-0},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BahrNKNVICM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BeckNMKR21,
author = {Michael Edmund Beck and
Jacopo Negroni and
Svend Matthiesen and
Michael Kohnen and
Christoph Riplinger},
title = {A binding mode hypothesis for prothioconazole binding to {CYP51} derived
from first principles quantum chemistry},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {4},
pages = {493--503},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00331-z},
doi = {10.1007/S10822-020-00331-Z},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BeckNMKR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BergazinBLGGM21,
author = {Teresa Danielle Bergazin and
Ido Y. Ben{-}Shalom and
Nathan M. Lim and
Sam C. Gill and
Michael K. Gilson and
David L. Mobley},
title = {Enhancing water sampling of buried binding sites using nonequilibrium
candidate Monte Carlo},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {2},
pages = {167--177},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00344-8},
doi = {10.1007/S10822-020-00344-8},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BergazinBLGGM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BergazinTZMGFBK21,
author = {Teresa Danielle Bergazin and
Nicolas Tielker and
Yingying Zhang and
Junjun Mao and
Marilyn R. Gunner and
Karol Francisco and
Carlo Ballatore and
Stefan M. Kast and
David L. Mobley},
title = {Evaluation of log P, pK\({}_{\mbox{a}}\), and log {D} predictions
from the {SAMPL7} blind challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {7},
pages = {771--802},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00397-3},
doi = {10.1007/S10822-021-00397-3},
timestamp = {Thu, 12 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BergazinTZMGFBK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BorbulevychMW21,
author = {Oleg Y. Borbulevych and
Roger I. Martin and
Lance M. Westerhoff},
title = {The critical role of {QM/MM} X-ray refinement and accurate tautomer/protomer
determination in structure-based drug design},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {4},
pages = {433--451},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00354-6},
doi = {10.1007/S10822-020-00354-6},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BorbulevychMW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CasbarraP21,
author = {Lorenzo Casbarra and
Piero Procacci},
title = {Binding free energy predictions in host-guest systems using Autodock4.
{A} retrospective analysis on SAMPL6, {SAMPL7} and {SAMPL8} challenges},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {6},
pages = {721--729},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00388-4},
doi = {10.1007/S10822-021-00388-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CasbarraP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DeganuttiPR21,
author = {Giuseppe Deganutti and
Filippo Prischi and
Christopher A. Reynolds},
title = {Supervised molecular dynamics for exploring the druggability of the
SARS-CoV-2 spike protein},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {2},
pages = {195--207},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00356-4},
doi = {10.1007/S10822-020-00356-4},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DeganuttiPR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Demerdash21,
author = {Omar N. A. Demerdash},
title = {Using diverse potentials and scoring functions for the development
of improved machine-learned models for protein-ligand affinity and
docking pose prediction},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {11},
pages = {1095--1123},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00423-4},
doi = {10.1007/S10822-021-00423-4},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Demerdash21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DonyapourD21,
author = {Nazanin Donyapour and
Alex Dickson},
title = {Predicting partition coefficients for the {SAMPL7} physical property
challenge using the ClassicalGSG method},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {7},
pages = {819--830},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00400-x},
doi = {10.1007/S10822-021-00400-X},
timestamp = {Thu, 12 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DonyapourD21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/EhrmanLBTKM21,
author = {Jordan N. Ehrman and
Victoria T. Lim and
Caitlin C. Bannan and
Nam Thi and
Daisy Y. Kyu and
David L. Mobley},
title = {Improving small molecule force fields by identifying and characterizing
small molecules with inconsistent parameters},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {3},
pages = {271--284},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00367-1},
doi = {10.1007/S10822-020-00367-1},
timestamp = {Wed, 07 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/EhrmanLBTKM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/EkenAWW21,
author = {Yigitcan Eken and
Nuno M. S. Almeida and
Cong Wang and
Angela K. Wilson},
title = {{SAMPL7:} Host-guest binding prediction by molecular dynamics and
quantum mechanics},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {1},
pages = {63--77},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00357-3},
doi = {10.1007/S10822-020-00357-3},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/EkenAWW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FalcioniKH21,
author = {Fabio Falcioni and
Jas Kalayan and
Richard H. Henchman},
title = {Energy-entropy prediction of octanol-water logP of {SAMPL7} N-acyl
sulfonamide bioisosters},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {7},
pages = {831--840},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00401-w},
doi = {10.1007/S10822-021-00401-W},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FalcioniKH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FanNVIB21,
author = {Shujie Fan and
Hristo Nedev and
Ranjit Vijayan and
Bogdan I. Iorga and
Oliver Beckstein},
title = {Precise force-field-based calculations of octanol-water partition
coefficients for the {SAMPL7} molecules},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {7},
pages = {853--870},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00407-4},
doi = {10.1007/S10822-021-00407-4},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/FanNVIB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FindikHAA21,
author = {Basak Koca Findik and
Zeynep Pinar Haslak and
Evrim Arslan and
Viktorya Aviyente},
title = {{SAMPL7} blind challenge: quantum-mechanical prediction of partition
coefficients and acid dissociation constants for small drug-like molecules},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {7},
pages = {841--851},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00402-9},
doi = {10.1007/S10822-021-00402-9},
timestamp = {Thu, 12 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FindikHAA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GeMZWSYWLY21,
author = {Huizhen Ge and
Longfei Mao and
Jie Zhao and
Yuwei Wang and
Danfeng Shi and
Xing Yang and
Xiaorui Wang and
Huanxiang Liu and
Xiaojun Yao},
title = {Discovery of novel {IDO1} inhibitors via structure-based virtual screening
and biological assays},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {5},
pages = {679--694},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00386-6},
doi = {10.1007/S10822-021-00386-6},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GeMZWSYWLY21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GhorbaniHJAMKB21,
author = {Mahdi Ghorbani and
Phillip S. Hudson and
Michael R. Jones and
F{\'{e}}lix Aviat and
Rub{\'{e}}n Meana{-}Pa{\~{n}}eda and
Jeffery B. Klauda and
Bernard R. Brooks},
title = {A replica exchange umbrella sampling {(REUS)} approach to predict
host-guest binding free energies in {SAMPL8} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {5},
pages = {667--677},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00385-7},
doi = {10.1007/S10822-021-00385-7},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GhorbaniHJAMKB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Goller21,
author = {Andreas H. G{\"{o}}ller},
title = {Editorial special issue on "Quantum Mechanics in Industry"},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {4},
pages = {397--398},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00373-x},
doi = {10.1007/S10822-021-00373-X},
timestamp = {Wed, 21 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Goller21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GonzalezSAGPOL21,
author = {Jorge Enrique Hern{\'{a}}ndez Gonz{\'{a}}lez and
Emir Salas{-}Sarduy and
Lilian Hern{\'{a}}ndez Alvarez and
Diego Enry Barreto Gomes and
Pedro Geraldo Pascutti and
Chris Oostenbrink and
Vitor B. P. Leite},
title = {In silico identification of noncompetitive inhibitors targeting an
uncharacterized allosteric site of falcipain-2},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {10},
pages = {1067--1079},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00420-7},
doi = {10.1007/S10822-021-00420-7},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GonzalezSAGPOL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HamedSZ21,
author = {Mazen Y. Hamed and
Reema Siam and
Roza Zaid},
title = {The role of zinc finger linkers in zinc finger protein binding to
{DNA}},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {9},
pages = {973--986},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00413-6},
doi = {10.1007/S10822-021-00413-6},
timestamp = {Tue, 05 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HamedSZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HasanASK21,
author = {Md. Mehedi Hasan and
Md. Ashad Alam and
Watshara Shoombuatong and
Hiroyuki Kurata},
title = {IRC-Fuse: improved and robust prediction of redox-sensitive cysteine
by fusing of multiple feature representations},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {3},
pages = {315--323},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00368-0},
doi = {10.1007/S10822-020-00368-0},
timestamp = {Wed, 07 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HasanASK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HermannPGWT21,
author = {Markus R. Hermann and
Alexander Pautsch and
Marc A. Grundl and
Alexander Weber and
Christofer S. Tautermann},
title = {Covalent inhibitor reactivity prediction by the electrophilicity index
- in and out of scope},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {4},
pages = {531--539},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00342-w},
doi = {10.1007/S10822-020-00342-W},
timestamp = {Wed, 22 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/HermannPGWT21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Hernandez-Alvarado21,
author = {R. Bruno Hern{\'{a}}ndez{-}Alvarado and
Abraham Madariaga{-}Maz{\'{o}}n and
Fernando Cosme{-}Vela and
Andr{\'{e}}s F. Marmolejo{-}Valencia and
Adel Nefzi and
Karina Mart{\'{\i}}nez{-}Mayorga},
title = {Encoding mu-opioid receptor biased agonism with interaction fingerprints},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {11},
pages = {1081--1093},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00422-5},
doi = {10.1007/S10822-021-00422-5},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Hernandez-Alvarado21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HuaiYLS21,
author = {Zhe Huai and
Huaiyu Yang and
Xiao Li and
Zhaoxi Sun},
title = {{SAMPL7} TrimerTrip host-guest binding affinities from extensive alchemical
and end-point free energy calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {1},
pages = {117--129},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00351-9},
doi = {10.1007/S10822-020-00351-9},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HuaiYLS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HuaiYS21,
author = {Zhe Huai and
Huaiyu Yang and
Zhaoxi Sun},
title = {Binding thermodynamics and interaction patterns of human purine nucleoside
phosphorylase-inhibitor complexes from extensive free energy calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {5},
pages = {643--656},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00382-w},
doi = {10.1007/S10822-021-00382-W},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HuaiYS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/InnokHCRK21,
author = {Wansiri Innok and
Asadhawut Hiranrat and
Netnapa Chana and
Thanyada Rungrotmongkol and
Panita Kongsune},
title = {In silico and in vitro anti-AChE activity investigations of constituents
from Mytragyna speciosa for Alzheimer's disease treatment},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {3},
pages = {325--336},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00372-4},
doi = {10.1007/S10822-020-00372-4},
timestamp = {Wed, 07 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/InnokHCRK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/IqbalVB21,
author = {Javed Iqbal and
Martin Vogt and
J{\"{u}}rgen Bajorath},
title = {Prediction of activity cliffs on the basis of images using convolutional
neural networks},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {12},
pages = {1157--1164},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00380-y},
doi = {10.1007/S10822-021-00380-Y},
timestamp = {Wed, 15 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/IqbalVB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/IsikRRGMC21,
author = {Mehtap Isik and
Ari{\"{e}}n S. Rustenburg and
Andrea Rizzi and
Marilyn R. Gunner and
David L. Mobley and
John D. Chodera},
title = {Overview of the {SAMPL6} pK\({}_{\mbox{a}}\) challenge: evaluating
small molecule microscopic and macroscopic pK\({}_{\mbox{a}}\) predictions},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {2},
pages = {131--166},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00362-6},
doi = {10.1007/S10822-020-00362-6},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/IsikRRGMC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KellettSSDG21,
author = {K. Kellett and
David R. Slochower and
Michael Schauperl and
B. M. Duggan and
Michael K. Gilson},
title = {Experimental characterization of the association of {\(\beta\)}-cyclodextrin
and eight novel cyclodextrin derivatives with two guest compounds},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {1},
pages = {95--104},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00350-w},
doi = {10.1007/S10822-020-00350-W},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KellettSSDG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KhalafPRAISSGFP21,
author = {Noureddine Ben Khalaf and
Susie Pham and
Giuseppe Romeo and
Sara Abdelghany and
Sebastiano Intagliata and
Peter Sedillo and
Loredana Salerno and
Jessica Gonzales and
Dahmani M. Fathallah and
Douglas J. Perkins and
Ivy Hurwitz and
Valeria Pittal{\`{a}}},
title = {A computer-aided approach to identify novel Leishmania major protein
disulfide isomerase inhibitors for treatment of leishmaniasis},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {3},
pages = {297--314},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00374-w},
doi = {10.1007/S10822-021-00374-W},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KhalafPRAISSGFP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KhalakTGG21,
author = {Yuriy Khalak and
Gary Tresadern and
Bert L. de Groot and
Vytautas Gapsys},
title = {Non-equilibrium approach for binding free energies in cyclodextrins
in {SAMPL7:} force fields and software},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {1},
pages = {49--61},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00359-1},
doi = {10.1007/S10822-020-00359-1},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KhalakTGG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Kim21,
author = {Ki Hwan Kim},
title = {Outliers in {SAR} and {QSAR:} 3. Importance of considering the role
of water molecules in protein-ligand interactions and quantitative
structure-activity relationship studies},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {3},
pages = {371--396},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00377-7},
doi = {10.1007/S10822-021-00377-7},
timestamp = {Wed, 07 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Kim21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KovalishynZKZKH21,
author = {Vasyl V. Kovalishyn and
Volodymyr Zyabrev and
Maryna V. Kachaeva and
Kostiantyn Ziabrev and
Kathy Keith and
Emma Harden and
Caroll Hartline and
Scott H. James and
Volodymyr Brovarets},
title = {Design of new imidazole derivatives with anti-HCMV activity: {QSAR}
modeling, synthesis and biological testing},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {12},
pages = {1177--1187},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00428-z},
doi = {10.1007/S10822-021-00428-Z},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KovalishynZKZKH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LenselinkS21,
author = {Eelke B. Lenselink and
Pieter F. W. Stouten},
title = {Multitask machine learning models for predicting lipophilicity (logP)
in the {SAMPL7} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {8},
pages = {901--909},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00405-6},
doi = {10.1007/S10822-021-00405-6},
timestamp = {Wed, 01 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LenselinkS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LevineWJDYB21,
author = {Daniel S. Levine and
Mark A. Watson and
Leif D. Jacobson and
Claire E. Dickerson and
Haoyu S. Yu and
Art D. Bochevarov},
title = {Pattern-free generation and quantum mechanical scoring of ring-chain
tautomers},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {4},
pages = {417--431},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00334-w},
doi = {10.1007/S10822-020-00334-W},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LevineWJDYB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Lewis21,
author = {Richard A. Lewis},
title = {Best practices for repurposing studies},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {12},
pages = {1189--1193},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00430-5},
doi = {10.1007/S10822-021-00430-5},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Lewis21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiefferingeKWP21,
author = {Fran{\c{c}}ois Van Liefferinge and
Eva{-}Maria Krammer and
Jehan Waeytens and
Martine Pr{\'{e}}vost},
title = {Molecular mechanism of thiamine pyrophosphate import into mitochondria:
a molecular simulation study},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {9},
pages = {987--1007},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00414-5},
doi = {10.1007/S10822-021-00414-5},
timestamp = {Fri, 25 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LiefferingeKWP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LizanaUD21,
author = {Ignacio Lizana and
Elena A. Uribe and
Eduardo J. Delgado},
title = {A theoretical approach for the acylation/deacylation mechanisms of
avibactam in the reversible inhibition of {KPC-2}},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {9},
pages = {943--952},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00408-3},
doi = {10.1007/S10822-021-00408-3},
timestamp = {Tue, 05 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LizanaUD21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LopezPZ21,
author = {Kenneth Lopez and
Silvana Pinheiro and
William J. Zamora},
title = {Multiple linear regression models for predicting the n{\unicode{8209}}octanol/water
partition coefficients in the {SAMPL7} blind challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {8},
pages = {923--931},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00409-2},
doi = {10.1007/S10822-021-00409-2},
timestamp = {Wed, 01 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LopezPZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LuiseRS21,
author = {Chiara Luise and
Dina Robaa and
Wolfgang Sippl},
title = {Exploring aromatic cage flexibility of the histone methyllysine reader
protein Spindlin1 and its impact on binding mode prediction: an in
silico study},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {6},
pages = {695--706},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00391-9},
doi = {10.1007/S10822-021-00391-9},
timestamp = {Fri, 23 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LuiseRS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LukacWGZ21,
author = {Iva Lukac and
Paul G. Wyatt and
Ian H. Gilbert and
Fabio Zuccotto},
title = {Ligand binding: evaluating the contribution of the water molecules
network using the Fragment Molecular Orbital method},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {10},
pages = {1025--1036},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00416-3},
doi = {10.1007/S10822-021-00416-3},
timestamp = {Wed, 03 Nov 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LukacWGZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MahmoudICVKWMBC21,
author = {Samar Mahmoud and
Benedict W. J. Irwin and
Dmitriy Chekmarev and
Shyam Vyas and
Jeff Kattas and
Thomas M. Whitehead and
Tamsin Mansley and
Jack Bikker and
Gareth John Conduit and
Matthew D. Segall},
title = {Imputation of sensory properties using deep learning},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {11},
pages = {1125--1140},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00424-3},
doi = {10.1007/S10822-021-00424-3},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MahmoudICVKWMBC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MalikCPNCS21,
author = {Aijaz Ahmad Malik and
Warot Chotpatiwetchkul and
Chuleeporn Phanus{-}umporn and
Chanin Nantasenamat and
Phasit Charoenkwan and
Watshara Shoombuatong},
title = {StackHCV: a web-based integrative machine-learning framework for large-scale
identification of hepatitis {C} virus {NS5B} inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {10},
pages = {1037--1053},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00418-1},
doi = {10.1007/S10822-021-00418-1},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MalikCPNCS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MarchandPES21,
author = {Jean{-}R{\'{e}}my Marchand and
Bernard Pirard and
Peter Ertl and
Finton Sirockin},
title = {{CAVIAR:} a method for automatic cavity detection, description and
decomposition into subcavities},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {6},
pages = {737--750},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00390-w},
doi = {10.1007/S10822-021-00390-W},
timestamp = {Tue, 13 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MarchandPES21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MillsG21,
author = {Alberto Mills and
Federico Gago},
title = {Insight into the sequence-specific elements leading to increased {DNA}
bending and ligase-mediated circularization propensity by antitumor
trabectedin},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {6},
pages = {707--719},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00396-4},
doi = {10.1007/S10822-021-00396-4},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MillsG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MisawaYH21,
author = {Kensuke Misawa and
Noriyuki Yamaotsu and
Shuichi Hirono},
title = {Identification of novel {EED-EZH2} {PPI} inhibitors using an in silico
fragment mapping method},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {5},
pages = {601--611},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00378-6},
doi = {10.1007/S10822-021-00378-6},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MisawaYH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MorawietzA21,
author = {Tobias Morawietz and
Nongnuch Artrith},
title = {Machine learning-accelerated quantum mechanics-based atomistic simulations
for industrial applications},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {4},
pages = {557--586},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00346-6},
doi = {10.1007/S10822-020-00346-6},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MorawietzA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OerenWHPS21,
author = {Mario {\"{O}}eren and
Peter J. Walton and
Peter A. Hunt and
David J. Ponting and
Matthew D. Segall},
title = {Predicting reactivity to drug metabolism: beyond P450s - modelling
FMOs and UGTs},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {4},
pages = {541--555},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00321-1},
doi = {10.1007/S10822-020-00321-1},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OerenWHPS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PihanKRBG21,
author = {Emilie Pihan and
Martin Kotev and
Obdulia Rabal and
Claudia Beato and
Constantino Diaz Gonzalez},
title = {Fine tuning for success in structure-based virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {12},
pages = {1195--1206},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00431-4},
doi = {10.1007/S10822-021-00431-4},
timestamp = {Wed, 15 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/PihanKRBG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PlogerKMG21,
author = {Tobias A. Pl{\"{o}}ger and
Stefan Koep and
Hans{-}Christian Militzer and
Andreas H. G{\"{o}}ller},
title = {Combined experimental and quantum mechanical elucidation of the synthetically
accessible stereoisomers of Hydroxyestradienone (HED), the starting
material for vilaprisan synthesis},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {4},
pages = {505--516},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00353-7},
doi = {10.1007/S10822-020-00353-7},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PlogerKMG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ProcacciG21,
author = {Piero Procacci and
Guido Guarnieri},
title = {{SAMPL7} blind predictions using nonequilibrium alchemical approaches},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {1},
pages = {37--47},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00365-3},
doi = {10.1007/S10822-020-00365-3},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ProcacciG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ProcacciM21,
author = {Piero Procacci and
Marina Macchiagodena},
title = {On the {NS-DSSB} unidirectional estimates in the {SAMPL6} SAMPLing
challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {10},
pages = {1055--1065},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00419-0},
doi = {10.1007/S10822-021-00419-0},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ProcacciM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RaddiV21,
author = {Robert M. Raddi and
Vincent A. Voelz},
title = {Stacking Gaussian processes to improve pK\({}_{\mbox{a}}\) predictions
in the {SAMPL7} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {9},
pages = {953--961},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00411-8},
doi = {10.1007/S10822-021-00411-8},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RaddiV21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Rodriguez-Perez21,
author = {Raquel Rodr{\'{\i}}guez{-}P{\'{e}}rez and
J{\"{u}}rgen Bajorath},
title = {Evaluation of multi-target deep neural network models for compound
potency prediction under increasingly challenging test conditions},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {3},
pages = {285--295},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00376-8},
doi = {10.1007/S10822-021-00376-8},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Rodriguez-Perez21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Rosell-HidalgoY21,
author = {Alicia Rosell{-}Hidalgo and
Luke Young and
Anthony L. Moore and
Taravat Ghafourian},
title = {{QSAR} and molecular docking for the search of {AOX} inhibitors: a
rational drug discovery approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {2},
pages = {245--260},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00360-8},
doi = {10.1007/S10822-020-00360-8},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Rosell-HidalgoY21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RoyDWK21,
author = {Dipankar Roy and
Devjyoti Dutta and
David S. Wishart and
Andriy Kovalenko},
title = {Predicting {PAMPA} permeability using the 3D-RISM-KH theory: are we
there yet?},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {2},
pages = {261--269},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00364-4},
doi = {10.1007/S10822-020-00364-4},
timestamp = {Tue, 23 Mar 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/RoyDWK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SabatinoP21,
author = {Spencer J. Sabatino and
Andrew S. Paluch},
title = {Predicting octanol/water partition coefficients using molecular simulation
for the {SAMPL7} challenge: comparing the use of neat and water saturated
1-octanol},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {10},
pages = {1009--1024},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00415-4},
doi = {10.1007/S10822-021-00415-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SabatinoP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Sahakyan21,
author = {Harutyun Sahakyan},
title = {Improving virtual screening results with {MM/GBSA} and {MM/PBSA} rescoring},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {6},
pages = {731--736},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00389-3},
doi = {10.1007/S10822-021-00389-3},
timestamp = {Tue, 13 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Sahakyan21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SakaguchiOT21,
author = {Kaori Sakaguchi and
Yoshio Okiyama and
Shigenori Tanaka},
title = {In silico modeling of PAX8-PPAR{\(\gamma\)} fusion protein in thyroid
carcinoma: influence of structural perturbation by fusion on ligand-binding
affinity},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {5},
pages = {629--642},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00381-x},
doi = {10.1007/S10822-021-00381-X},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SakaguchiOT21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SatoMJF21,
author = {Akinori Sato and
Tomoyuki Miyao and
Swarit Jasial and
Kimito Funatsu},
title = {Comparing predictive ability of {QSAR/QSPR} models using 2D and 3D
molecular representations},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {2},
pages = {179--193},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00361-7},
doi = {10.1007/S10822-020-00361-7},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SatoMJF21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ScarpinoPKIAFGK21,
author = {Andrea Scarpino and
L{\'{a}}szl{\'{o}} Petri and
Damijan Knez and
T{\'{\i}}mea Imre and
P{\'{e}}ter {\'{A}}br{\'{a}}nyi{-}Balogh and
Gy{\"{o}}rgy G. Ferenczy and
Stanislav Gobec and
Gy{\"{o}}rgy M. Keser{\"{u}}},
title = {{WIDOCK:} a reactive docking protocol for virtual screening of covalent
inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {2},
pages = {223--244},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00371-5},
doi = {10.1007/S10822-020-00371-5},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ScarpinoPKIAFGK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Schindler21,
author = {Michael Schindler},
title = {Investigations on the E/Z-isomerism of neonicotinoids},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {4},
pages = {517--529},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00326-w},
doi = {10.1007/S10822-020-00326-W},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Schindler21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SerillonBB21,
author = {Dylan Serillon and
Carles Bo and
Xavier Barril},
title = {Testing automatic methods to predict free binding energy of host-guest
complexes in {SAMPL7} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {2},
pages = {209--222},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00370-6},
doi = {10.1007/S10822-020-00370-6},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SerillonBB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ShahraniAAHR21,
author = {Mesfer Al Shahrani and
Mohammad Abohassan and
Mohammad Y. Alshahrani and
Abdulrahim R. Hakami and
Prasanna Rajagopalan},
title = {High-throughput virtual screening and preclinical analysis identifies
CB-1, a novel potent dual B-Raf/c-Raf inhibitor, effective against
wild and mutant variants of B-Raf expression in colorectal carcinoma},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {12},
pages = {1165--1176},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00426-1},
doi = {10.1007/S10822-021-00426-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ShahraniAAHR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ShiLWP21,
author = {Yuanjun Shi and
Marie L. Laury and
Zhi Wang and
Jay W. Ponder},
title = {{AMOEBA} binding free energies for the {SAMPL7} TrimerTrip host-guest
challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {1},
pages = {79--93},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00358-2},
doi = {10.1007/S10822-020-00358-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ShiLWP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/StantonBMP21,
author = {David T. Stanton and
Jennifer R. Baker and
Adam McCluskey and
Stefan Paula},
title = {Development and interpretation of a {QSAR} model for in vitro breast
cancer {(MCF-7)} cytotoxicity of 2-phenylacrylonitriles},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {5},
pages = {613--628},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00387-5},
doi = {10.1007/S10822-021-00387-5},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/StantonBMP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Sun21,
author = {Zhaoxi Sun},
title = {{SAMPL7} TrimerTrip host-guest binding poses and binding affinities
from spherical-coordinates-biased simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {1},
pages = {105--115},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00335-9},
doi = {10.1007/S10822-020-00335-9},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Sun21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SureMPD21,
author = {Rebecca Sure and
Moad el Mahdali and
Alex Plajer and
Peter Deglmann},
title = {Towards a converged strategy for including microsolvation in reaction
mechanism calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {4},
pages = {473--492},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00366-2},
doi = {10.1007/S10822-020-00366-2},
timestamp = {Thu, 29 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SureMPD21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TanooriJM21,
author = {Betsabeh Tanoori and
Mansoor Zolghadri Jahromi and
Eghbal G. Mansoori},
title = {Binding affinity prediction for binary drug-target interactions using
semi-supervised transfer learning},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {8},
pages = {883--900},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00404-7},
doi = {10.1007/S10822-021-00404-7},
timestamp = {Wed, 01 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TanooriJM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TeixeiraLFNC21,
author = {Olivia Teixeira and
Pedro Lacerda and
Thamires Quadros Froes and
Maria Cristina Nonato and
Marcelo Santos Castilho},
title = {Druggable hot spots in trypanothione reductase: novel insights and
opportunities for drug discovery revealed by DRUGpy},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {8},
pages = {871--882},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00403-8},
doi = {10.1007/S10822-021-00403-8},
timestamp = {Wed, 01 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TeixeiraLFNC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TielkerEHSGK21,
author = {Nicolas Tielker and
Lukas Eberlein and
Gerhard Hessler and
K. Friedemann Schmidt and
Stefan G{\"{u}}ssregen and
Stefan M. Kast},
title = {Quantum-mechanical property prediction of solvated drug molecules:
what have we learned from a decade of {SAMPL} blind prediction challenges?},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {4},
pages = {453--472},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00347-5},
doi = {10.1007/S10822-020-00347-5},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TielkerEHSGK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TielkerGK21,
author = {Nicolas Tielker and
Stefan G{\"{u}}ssregen and
Stefan M. Kast},
title = {{SAMPL7} physical property prediction from {EC-RISM} theory},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {8},
pages = {933--941},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00410-9},
doi = {10.1007/S10822-021-00410-9},
timestamp = {Wed, 01 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TielkerGK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TophamS21,
author = {Christopher M. Topham and
Jeremy C. Smith},
title = {Peptide nucleic acid Hoogsteen strand linker design for major groove
recognition of {DNA} thymine bases},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {3},
pages = {355--369},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00375-9},
doi = {10.1007/S10822-021-00375-9},
timestamp = {Wed, 07 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TophamS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TripathiLVL21,
author = {Neha Tripathi and
Laurence Leherte and
Daniel P. Vercauteren and
Ad{\`{e}}le D. Laurent},
title = {Structure-based identification of inhibitors disrupting the {CD2-CD58}
interactions},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {3},
pages = {337--353},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00369-z},
doi = {10.1007/S10822-020-00369-Z},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TripathiLVL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/UdvarhelyiRW21,
author = {Anik{\'{o}} Udvarhelyi and
Stephane Rodde and
Rainer Wilcken},
title = {ReSCoSS: a flexible quantum chemistry workflow identifying relevant
solution conformers of drug-like molecules},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {4},
pages = {399--415},
year = {2021},
url = {https://doi.org/10.1007/s10822-020-00337-7},
doi = {10.1007/S10822-020-00337-7},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/UdvarhelyiRW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ViaynaPCLZ21,
author = {Antonio Viayna and
Silvana Pinheiro and
Carles Curutchet and
F. Javier Luque and
William J. Zamora},
title = {Prediction of n-octanol/water partition coefficients and acidity constants
(pK\({}_{\mbox{a}}\)) in the {SAMPL7} blind challenge with the {IEFPCM-MST}
model},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {7},
pages = {803--811},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00394-6},
doi = {10.1007/S10822-021-00394-6},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ViaynaPCLZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WangMP21,
author = {Yuhang Wang and
Sruthi Murlidaran and
David A. Pearlman},
title = {Quantum simulations of SARS-CoV-2 main protease M\({}^{\mbox{pro}}\)
enable high-quality scoring of diverse ligands},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {9},
pages = {963--971},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00412-7},
doi = {10.1007/S10822-021-00412-7},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/WangMP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WarnauWR21,
author = {Judith Warnau and
Karin Wichmann and
Jens Reinisch},
title = {{COSMO-RS} predictions of logP in the {SAMPL7} blind challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {7},
pages = {813--818},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00395-5},
doi = {10.1007/S10822-021-00395-5},
timestamp = {Thu, 12 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WarnauWR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YoshimoriHB21,
author = {Atsushi Yoshimori and
Huabin Hu and
J{\"{u}}rgen Bajorath},
title = {Adapting the DeepSARM approach for dual-target ligand design},
journal = {J. Comput. Aided Mol. Des.},
volume = {35},
number = {5},
pages = {587--600},
year = {2021},
url = {https://doi.org/10.1007/s10822-021-00379-5},
doi = {10.1007/S10822-021-00379-5},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YoshimoriHB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AbdoGAP20,
author = {Ammar Abdo and
Eissa Ghaleb and
Naser K. A. Alajmi and
Maude Pupin},
title = {Monomer structure fingerprints: an extension of the monomer composition
version for peptide databases},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {11},
pages = {1147--1156},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00336-8},
doi = {10.1007/S10822-020-00336-8},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AbdoGAP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AghazadehKRB20,
author = {Hossein Aghazadeh and
Mokhtar Ganjali Koli and
Reza Ranjbar and
Kamran Pooshang Bagheri},
title = {Interactions of {GF-17} derived from {LL-37} antimicrobial peptide
with bacterial membranes: a molecular dynamics simulation study},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {12},
pages = {1261--1273},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00348-4},
doi = {10.1007/S10822-020-00348-4},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AghazadehKRB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ArifAAFLY20,
author = {Muhammad Arif and
Saeed Ahmad and
Farman Ali and
Ge Fang and
Min Li and
Dong{-}Jun Yu},
title = {TargetCPP: accurate prediction of cell-penetrating peptides from optimized
multi-scale features using gradient boost decision tree},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {8},
pages = {841--856},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00307-z},
doi = {10.1007/S10822-020-00307-Z},
timestamp = {Sun, 30 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ArifAAFLY20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ArslanFA20,
author = {Evrim Arslan and
Basak Koca Findik and
Viktorya Aviyente},
title = {A blind {SAMPL6} challenge: insight into the octanol-water partition
coefficients of drug-like molecules via a {DFT} approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {4},
pages = {463--470},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00284-3},
doi = {10.1007/S10822-020-00284-3},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ArslanFA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AshidaK20,
author = {Takeshi Ashida and
Takeshi Kikuchi},
title = {A new method for estimating the relative binding free energy, derived
from a free energy variational principle for the Pim-1-kinase-ligand
and FKBP-ligand systems},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {6},
pages = {647--658},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00302-4},
doi = {10.1007/S10822-020-00302-4},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AshidaK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AtanasioDR20,
author = {Silvia Atanasio and
Giuseppe Deganutti and
Christopher A. Reynolds},
title = {Addressing free fatty acid receptor 1 {(FFAR1)} activation using supervised
molecular dynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {11},
pages = {1181--1193},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00338-6},
doi = {10.1007/S10822-020-00338-6},
timestamp = {Fri, 25 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AtanasioDR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BasciuKMBV20,
author = {Andrea Basciu and
Panagiotis I. Koukos and
Giuliano Malloci and
Alexandre M. J. J. Bonvin and
Attilio Vittorio Vargiu},
title = {Coupling enhanced sampling of the apo-receptor with template-based
ligand conformers selection: performance in pose prediction in the
{D3R} Grand Challenge 4},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {2},
pages = {149--162},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00244-6},
doi = {10.1007/S10822-019-00244-6},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BasciuKMBV20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BaumgartnerE20,
author = {Matthew P. Baumgartner and
David A. Evans},
title = {Side chain virtual screening of matched molecular pairs: a PDB-wide
and ChEMBL-wide analysis},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {9},
pages = {953--963},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00313-1},
doi = {10.1007/S10822-020-00313-1},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BaumgartnerE20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BelgamoAPRRTCF20,
author = {Juli{\'{a}}n A. B{\'{e}}lgamo and
Lucas N. Alberca and
Jorge L. P{\'{o}}rfido and
Franco N. Caram Romero and
Santiago Rodriguez and
Alan Talevi and
Betina C{\'{o}}rsico and
Gisela R. Franchini},
title = {Application of target repositioning and in silico screening to exploit
fatty acid binding proteins (FABPs) from Echinococcus multilocularis
as possible drug targets},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {12},
pages = {1275--1288},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00352-8},
doi = {10.1007/S10822-020-00352-8},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BelgamoAPRRTCF20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BelloGR20,
author = {Martiniano Bello and
Concepci{\'{o}}n Guadarrama{-}Garc{\'{\i}}a and
Rolando Alberto Rodriguez{-}Fonseca},
title = {Dissecting the molecular recognition of dual lapatinib derivatives
for {EGFR/HER2}},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {3},
pages = {293--303},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00270-4},
doi = {10.1007/S10822-019-00270-4},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BelloGR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BorioniCPMPPG20,
author = {Jos{\'{e}} L. Borioni and
Valeria Cavallaro and
Adriana B. Pierini and
Ana Paula Murray and
Alicia B. Pe{\~{n}}{\'{e}}{\~{n}}ory and
Marcelo Puiatti and
Manuela E. Garc{\'{\i}}a},
title = {An activity prediction model for steroidal and triterpenoidal inhibitors
of Acetylcholinesterase enzyme},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {10},
pages = {1079--1090},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00324-y},
doi = {10.1007/S10822-020-00324-Y},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BorioniCPMPPG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BrownELLRS20,
author = {Nathan Brown and
Peter Ertl and
Richard A. Lewis and
Torsten Luksch and
Daniel Reker and
Nadine Schneider},
title = {Artificial intelligence in chemistry and drug design},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {7},
pages = {709--715},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00317-x},
doi = {10.1007/S10822-020-00317-X},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BrownELLRS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BufanoLBLNSBC20,
author = {Marianna Bufano and
Marion Laudette and
Jean{-}Paul Blondeau and
Frank Lezoualc'h and
Marianna Nalli and
Romano Silvestri and
Andrea Brancale and
Antonio Coluccia},
title = {Modeling Epac1 interactions with the allosteric inhibitor {AM-001}
by co-solvent molecular dynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {11},
pages = {1171--1179},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00332-y},
doi = {10.1007/S10822-020-00332-Y},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BufanoLBLNSBC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CharoenkwanNHS20,
author = {Phasit Charoenkwan and
Chanin Nantasenamat and
Md. Mehedi Hasan and
Watshara Shoombuatong},
title = {Meta-iPVP: a sequence-based meta-predictor for improving the prediction
of phage virion proteins using effective feature representation},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {10},
pages = {1105--1116},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00323-z},
doi = {10.1007/S10822-020-00323-Z},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CharoenkwanNHS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChenWSPY20,
author = {Jianzhong Chen and
Wei Wang and
Haibo Sun and
Laixue Pang and
Baohua Yin},
title = {Mutation-mediated influences on binding of anaplastic lymphoma kinase
to crizotinib decoded by multiple replica Gaussian accelerated molecular
dynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {12},
pages = {1289--1305},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00355-5},
doi = {10.1007/S10822-020-00355-5},
timestamp = {Fri, 25 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ChenWSPY20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ClarkMCLPRLFGGW20,
author = {Robert D. Clark and
Denise N. Morris and
Gary Chinigo and
Michael S. Lawless and
Jacques Prudhomme and
Karine G. Le Roch and
Maria Jos{\'{e}} Lafuente and
Santiago Ferrer and
Francisco Javier Gamo and
Robert Gadwood and
Walter S. Woltosz},
title = {Design and tests of prospective property predictions for novel antimalarial
2-aminopropylaminoquinolones},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {11},
pages = {1117--1132},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00333-x},
doi = {10.1007/S10822-020-00333-X},
timestamp = {Fri, 25 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ClarkMCLPRLFGGW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ColodetteFMFSB20,
author = {Natalie M. Colodette and
Lucas S. Franco and
Rodolfo C. Maia and
Harold H. Fokoue and
Carlos Mauricio R. Sant'Anna and
Eliezer J. Barreiro},
title = {Novel phosphatidylinositol 4-kinases {III} beta (PI4KIII{\(\beta\)})
inhibitors discovered by virtual screening using free energy models},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {10},
pages = {1091--1103},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00327-9},
doi = {10.1007/S10822-020-00327-9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ColodetteFMFSB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DingXQCZHSH20,
author = {Ye Ding and
You Xu and
Cheng Qian and
Jinfeng Chen and
Jian Zhu and
Houhou Huang and
Yi Shi and
Jing Huang},
title = {Predicting partition coefficients of drug-like molecules in the {SAMPL6}
challenge with Drude polarizable force fields},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {4},
pages = {421--435},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00282-5},
doi = {10.1007/S10822-020-00282-5},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DingXQCZHSH20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FanIB20,
author = {Shujie Fan and
Bogdan I. Iorga and
Oliver Beckstein},
title = {Prediction of octanol-water partition coefficients for the SAMPL6-log
{P} molecules using molecular dynamics simulations with OPLS-AA, {AMBER}
and {CHARMM} force fields},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {5},
pages = {543--560},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00267-z},
doi = {10.1007/S10822-019-00267-Z},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FanIB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GarciaTHG20,
author = {Gonzalo Cerruela Garc{\'{\i}}a and
Jos{\'{e}} P{\'{e}}rez{-}Parras Toledano and
Aida de Haro{-}Garc{\'{\i}}a and
Nicol{\'{a}}s Garc{\'{\i}}a{-}Pedrajas},
title = {Influence of feature rankers in the construction of molecular activity
prediction models},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {3},
pages = {305--325},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00273-1},
doi = {10.1007/S10822-019-00273-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GarciaTHG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GhiandoniBCHWWG20,
author = {Gian Marco Ghiandoni and
Michael J. Bodkin and
Beining Chen and
Dimitar Hristozov and
James E. A. Wallace and
James Webster and
Valerie J. Gillet},
title = {Enhancing reaction-based de novo design using a multi-label reaction
class recommender},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {7},
pages = {783--803},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00300-6},
doi = {10.1007/S10822-020-00300-6},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GhiandoniBCHWWG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GilsonA20,
author = {Michael K. Gilson and
Rommie E. Amaro},
title = {Drug Design Data Resource, Grand Challenge 4, second of two issues},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {2},
pages = {97},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00296-z},
doi = {10.1007/S10822-020-00296-Z},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GilsonA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GreenPLSMMBPM20,
author = {Darren V. S. Green and
Stephen D. Pickett and
Christopher N. Luscombe and
Stefan Senger and
David Marcus and
Jamel Meslamani and
David Brett and
Adam Powell and
Jonathan Masson},
title = {{BRADSHAW:} a system for automated molecular design},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {7},
pages = {747--765},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00234-8},
doi = {10.1007/S10822-019-00234-8},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GreenPLSMMBPM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GreenPLSMMBPM20a,
author = {Darren V. S. Green and
Stephen D. Pickett and
Christopher N. Luscombe and
Stefan Senger and
David Marcus and
Jamel Meslamani and
David Brett and
Adam Powell and
Jonathan Masson},
title = {Correction to: {BRADSHAW:} a system for automated molecular design},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {7},
pages = {767},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00243-7},
doi = {10.1007/S10822-019-00243-7},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GreenPLSMMBPM20a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GuanLM20,
author = {Davy Guan and
Raymond Lui and
Slade Matthews},
title = {LogP prediction performance with the {SMD} solvation model and the
{M06} density functional family for {SAMPL6} blind prediction challenge
molecules},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {5},
pages = {511--522},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00278-1},
doi = {10.1007/S10822-020-00278-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GuanLM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GunnerMRIC20,
author = {Marilyn R. Gunner and
Taichi Murakami and
Ari{\"{e}}n S. Rustenburg and
Mehtap Isik and
John D. Chodera},
title = {Standard state free energies, not pK\({}_{\mbox{a}}\)s, are ideal
for describing small molecule protonation and tautomeric states},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {5},
pages = {561--573},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00280-7},
doi = {10.1007/S10822-020-00280-7},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GunnerMRIC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GureevNGVGT20,
author = {Maxim Gureev and
Daria Novikova and
Tatyana Grigoreva and
Svetlana Vorona and
Alexander Garabadzhiu and
Vyacheslav Tribulovich},
title = {Simulation of {MDM2} N-terminal domain conformational lability in
the presence of imidazoline based inhibitors of MDM2-p53 protein-protein
interaction},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {1},
pages = {55--70},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00260-6},
doi = {10.1007/S10822-019-00260-6},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GureevNGVGT20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HanpaiboolLTR20,
author = {Chonnikan Hanpaibool and
Matina Leelawiwat and
Kaito Takahashi and
Thanyada Rungrotmongkol},
title = {Source of oseltamivir resistance due to single {E119D} and double
{E119D/H274Y} mutations in pdm09H1N1 influenza neuraminidase},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {1},
pages = {27--37},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00251-7},
doi = {10.1007/S10822-019-00251-7},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/HanpaiboolLTR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HuB20,
author = {Huabin Hu and
J{\"{u}}rgen Bajorath},
title = {Simplified activity cliff network representations with high interpretability
and immediate access to {SAR} information},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {9},
pages = {943--952},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00319-9},
doi = {10.1007/S10822-020-00319-9},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HuB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/IsikBFRCM20,
author = {Mehtap Isik and
Teresa Danielle Bergazin and
Thomas Fox and
Andrea Rizzi and
John D. Chodera and
David L. Mobley},
title = {Assessing the accuracy of octanol-water partition coefficient predictions
in the {SAMPL6} Part {II} log {P} Challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {4},
pages = {335--370},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00295-0},
doi = {10.1007/S10822-020-00295-0},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/IsikBFRCM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/IsikLMRC20,
author = {Mehtap Isik and
Dorothy Levorse and
David L. Mobley and
Timothy Rhodes and
John D. Chodera},
title = {Octanol-water partition coefficient measurements for the {SAMPL6}
blind prediction challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {4},
pages = {405--420},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00271-3},
doi = {10.1007/S10822-019-00271-3},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/IsikLMRC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JonesB20,
author = {Michael R. Jones and
Bernard R. Brooks},
title = {Quantum chemical predictions of water-octanol partition coefficients
applied to the {SAMPL6} logP blind challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {5},
pages = {485--493},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00286-1},
doi = {10.1007/S10822-020-00286-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/JonesB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KadukovaCG20,
author = {Maria Kadukova and
Vladimir Chupin and
Sergei Grudinin},
title = {Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit
in the {D3R} Grand Challenge 4},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {2},
pages = {191--200},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00263-3},
doi = {10.1007/S10822-019-00263-3},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KadukovaCG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KhannaMDP20,
author = {Vikram Khanna and
Jacob I. Monroe and
Michael F. Doherty and
Baron Peters},
title = {Performing solvation free energy calculations in {LAMMPS} using the
decoupling approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {6},
pages = {641--646},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00303-3},
doi = {10.1007/S10822-020-00303-3},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KhannaMDP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KhatunHSK20,
author = {Mst. Shamima Khatun and
Md. Mehedi Hasan and
Watshara Shoombuatong and
Hiroyuki Kurata},
title = {ProIn-Fuse: improved and robust prediction of proinflammatory peptides
by fusing of multiple feature representations},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {12},
pages = {1229--1236},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00343-9},
doi = {10.1007/S10822-020-00343-9},
timestamp = {Wed, 07 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KhatunHSK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KotelnikovALIPB20,
author = {Sergei Kotelnikov and
Andrey Alekseenko and
Cong Liu and
Mikhail Ignatov and
Dzmitry Padhorny and
Emiliano Brini and
Mark Lukin and
Evangelos A. Coutsias and
Ken A. Dill and
Dima Kozakov},
title = {Sampling and refinement protocols for template-based macrocycle docking:
2018 {D3R} Grand Challenge 4},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {2},
pages = {179--189},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00257-1},
doi = {10.1007/S10822-019-00257-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KotelnikovALIPB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KovarSPMSBKZB20,
author = {Petr Kov{\'{a}}r and
Jakub Skoda and
Miroslav Posp{\'{\i}}sil and
Kl{\'{a}}ra Mel{\'{a}}nov{\'{a}} and
Jan Svoboda and
Ludv{\'{\i}}k Benes and
Petr Kut{\'{a}}lek and
V{\'{\i}}tezslav Zima and
Filip Bures},
title = {How N-(pyridin-4-yl)pyridin-4-amine and its methyl and nitro derivatives
are arranged in the interlayer space of zirconium sulfophenylphosphonate:
a problem solved by experimental and calculation methods},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {6},
pages = {683--695},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00299-w},
doi = {10.1007/S10822-020-00299-W},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KovarSPMSBKZB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KramerHJB20,
author = {Andreas Kr{\"{a}}mer and
Phillip S. Hudson and
Michael R. Jones and
Bernard R. Brooks},
title = {Multi-phase Boltzmann weighting: accounting for local inhomogeneity
in molecular simulations of water-octanol partition coefficients in
the {SAMPL6} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {5},
pages = {471--483},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00285-2},
doi = {10.1007/S10822-020-00285-2},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KramerHJB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KuderMKK20,
author = {Kamil J. Kuder and
Ilona Michalik and
Katarzyna Kiec{-}Kononowicz and
Peter Kolb},
title = {A Taxicab geometry quantification system to evaluate the performance
of in silico methods: a case study on adenosine receptors ligands},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {6},
pages = {697--707},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00301-5},
doi = {10.1007/S10822-020-00301-5},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KuderMKK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LansPCC20,
author = {Isaias Lans and
Karen Palacio{-}Rodr{\'{\i}}guez and
Claudio N. Cavasotto and
Pilar Cossio},
title = {Flexi-pharma: a molecule-ranking strategy for virtual screening using
pharmacophores from ligand-free conformational ensembles},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {10},
pages = {1063--1077},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00329-7},
doi = {10.1007/S10822-020-00329-7},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LansPCC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LinBHMV20,
author = {Arkadii I. Lin and
Bernd Beck and
Dragos Horvath and
Gilles Marcou and
Alexandre Varnek},
title = {Diversifying chemical libraries with generative topographic mapping},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {7},
pages = {805--815},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00215-x},
doi = {10.1007/S10822-019-00215-X},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LinBHMV20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuK20,
author = {Kai Liu and
Hironori Kokubo},
title = {Prediction of ligand binding mode among multiple cross-docking poses
by molecular dynamics simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {11},
pages = {1195--1205},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00340-y},
doi = {10.1007/S10822-020-00340-Y},
timestamp = {Fri, 25 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LiuK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Lopez-LopezROM20,
author = {Edgar L{\'{o}}pez{-}L{\'{o}}pez and
Obdulia Rabal and
Julen Oyarzabal and
Jos{\'{e}} L. Medina{-}Franco},
title = {Towards the understanding of the activity of G9a inhibitors: an activity
landscape and molecular modeling approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {6},
pages = {659--669},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00298-x},
doi = {10.1007/S10822-020-00298-X},
timestamp = {Tue, 16 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Lopez-LopezROM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LoschenRK20,
author = {Christoph Loschen and
Jens Reinisch and
Andreas Klamt},
title = {{COSMO-RS} based predictions for the {SAMPL6} logP challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {4},
pages = {385--392},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00259-z},
doi = {10.1007/S10822-019-00259-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LoschenRK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LuiGM20,
author = {Raymond Lui and
Davy Guan and
Slade Matthews},
title = {A comparison of molecular representations for lipophilicity quantitative
structure-property relationships with results from the {SAMPL6} logP
Prediction Challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {5},
pages = {523--534},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00279-0},
doi = {10.1007/S10822-020-00279-0},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LuiGM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MagantiB20,
author = {Lakshmi Maganti and
Dhananjay Bhattacharyya},
title = {Sequence specificity in DNA-drug intercalation: {MD} simulation and
density functional theory approaches},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {1},
pages = {83--95},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00268-y},
doi = {10.1007/S10822-019-00268-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MagantiB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MakarovM20,
author = {G. I. Makarov and
T. M. Makarova},
title = {A noncanonical binding site of linezolid revealed via molecular dynamics
simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {3},
pages = {281--291},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00269-x},
doi = {10.1007/S10822-019-00269-X},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MakarovM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MecklenfeldR20,
author = {Andreas Mecklenfeld and
Gabriele Raabe},
title = {Applicability of a thermodynamic cycle approach for a force field
parametrization targeting non-aqueous solvation free energies},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {1},
pages = {71--82},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00261-5},
doi = {10.1007/S10822-019-00261-5},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MecklenfeldR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MiljkovicB20,
author = {Filip Miljkovic and
J{\"{u}}rgen Bajorath},
title = {Data structures for computational compound promiscuity analysis and
exemplary applications to inhibitors of the human kinome},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {1},
pages = {1--10},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00266-0},
doi = {10.1007/S10822-019-00266-0},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/MiljkovicB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MillsG20,
author = {Alberto Mills and
Federico Gago},
title = {Atomistic insight into sequence-directed {DNA} bending and minicircle
formation propensity in the absence and presence of phased A-tracts},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {3},
pages = {253--265},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00288-z},
doi = {10.1007/S10822-020-00288-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MillsG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NguyenGWW20,
author = {Duc Duy Nguyen and
Kaifu Gao and
Menglun Wang and
Guo{-}Wei Wei},
title = {MathDL: mathematical deep learning for {D3R} Grand Challenge 4},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {2},
pages = {131--147},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00237-5},
doi = {10.1007/S10822-019-00237-5},
timestamp = {Mon, 01 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/NguyenGWW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NicolaKIA20,
author = {George Nicola and
Irina Kufareva and
Andrey V. Ilatovskiy and
Ruben Abagyan},
title = {Druggable exosites of the human kino-pocketome},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {3},
pages = {219--230},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00276-y},
doi = {10.1007/S10822-019-00276-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NicolaKIA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Nikitin20,
author = {Alexei M. Nikitin},
title = {Non-zero Lennard-Jones parameters for the Toukan-Rahman water model:
more accurate calculations of the solvation free energy of organic
substances},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {4},
pages = {437--441},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00256-2},
doi = {10.1007/S10822-019-00256-2},
timestamp = {Thu, 27 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Nikitin20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OlandersABK20,
author = {Gustav Olanders and
Hiba Alogheli and
Peter Brandt and
Anders Karl{\'{e}}n},
title = {Conformational analysis of macrocycles: comparing general and specialized
methods},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {3},
pages = {231--252},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00277-2},
doi = {10.1007/S10822-020-00277-2},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OlandersABK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OlsonCCGJHALMK20,
author = {Brian Olson and
Anthony Cruz{-}Balberdy and
Lieyang Chen and
Mossa Ghattas and
Yeonji Ji and
Kunhui Huang and
Steven Ayoub and
Tyler Luchko and
Daniel J. McKay and
Tom Kurtzman},
title = {An online repository of solvation thermodynamic and structural maps
of SARS-CoV-2 targets},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {12},
pages = {1219--1228},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00341-x},
doi = {10.1007/S10822-020-00341-X},
timestamp = {Thu, 16 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OlsonCCGJHALMK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OuimetP20,
author = {Jonathan A. Ouimet and
Andrew S. Paluch},
title = {Predicting octanol/water partition coefficients for the {SAMPL6} challenge
using the SM12, SM8, and {SMD} solvation models},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {5},
pages = {575--588},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00293-2},
doi = {10.1007/S10822-020-00293-2},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OuimetP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PaciottiACS20,
author = {Roberto Paciotti and
Mariangela Agamennone and
Cecilia Coletti and
Loriano Storchi},
title = {Characterization of {PD-L1} binding sites by a combined {FMO/GRID-DRY}
approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {8},
pages = {897--914},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00306-0},
doi = {10.1007/S10822-020-00306-0},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/PaciottiACS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParksGCYSWJMLBA20,
author = {Conor D. Parks and
Zied Gaieb and
Michael Chiu and
Huanwang Yang and
Chenghua Shao and
W. Patrick Walters and
Johanna M. Jansen and
Georgia B. McGaughey and
Richard A. Lewis and
Scott D. Bembenek and
Michael K. Ameriks and
Tara Mirzadegan and
Stephen K. Burley and
Rommie E. Amaro and
Michael K. Gilson},
title = {{D3R} grand challenge 4: blind prediction of protein-ligand poses,
affinity rankings, and relative binding free energies},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {2},
pages = {99--119},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00289-y},
doi = {10.1007/S10822-020-00289-Y},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ParksGCYSWJMLBA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PatelKJBW20,
author = {Prajay Patel and
David M. Kuntz and
Michael R. Jones and
Bernard R. Brooks and
Angela K. Wilson},
title = {{SAMPL6} logP challenge: machine learning and quantum mechanical approaches},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {5},
pages = {495--510},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00287-0},
doi = {10.1007/S10822-020-00287-0},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PatelKJBW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PathakDBCS20,
author = {Bani Kumar Pathak and
Debajyoti Das and
Sayan Bhakta and
Partha Chakrabarti and
Jayati Sengupta},
title = {Resveratrol as a nontoxic excipient stabilizes insulin in a bioactive
hexameric form},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {8},
pages = {915--927},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00311-3},
doi = {10.1007/S10822-020-00311-3},
timestamp = {Fri, 05 Nov 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/PathakDBCS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PeronaRMMG20,
author = {Almudena Perona and
M. Piedad Ros and
Alberto Mills and
Antonio Morreale and
Federico Gago},
title = {Distinct binding of cetirizine enantiomers to human serum albumin
and the human histamine receptor H\({}_{\mbox{1}}\)},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {10},
pages = {1045--1062},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00328-8},
doi = {10.1007/S10822-020-00328-8},
timestamp = {Sun, 11 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PeronaRMMG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PrasadB20,
author = {Samarjeet Prasad and
Bernard R. Brooks},
title = {A deep learning approach for the blind logP prediction in {SAMPL6}
challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {5},
pages = {535--542},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00292-3},
doi = {10.1007/S10822-020-00292-3},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PrasadB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Procacci20,
author = {Piero Procacci},
title = {A remark on the efficiency of the double-system/single-box nonequilibrium
approach in the {SAMPL6} SAMPLing challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {6},
pages = {635--639},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00312-2},
doi = {10.1007/S10822-020-00312-2},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Procacci20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ProcacciG20,
author = {Piero Procacci and
Guido Guarnieri},
title = {{SAMPL6} blind predictions of water-octanol partition coefficients
using nonequilibrium alchemical approaches},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {4},
pages = {371--384},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00233-9},
doi = {10.1007/S10822-019-00233-9},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ProcacciG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RaczK20,
author = {Anita R{\'{a}}cz and
Gy{\"{o}}rgy M. Keser{\"{u}}},
title = {Large-scale evaluation of cytochrome {P450} 2C9 mediated drug interaction
potential with machine learning-based consensus modeling},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {8},
pages = {831--839},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00308-y},
doi = {10.1007/S10822-020-00308-Y},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RaczK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RajanR20,
author = {Ravi Kumar Rajan and
Muthiah Ramanathan},
title = {Identification and neuroprotective evaluation of a potential c-Jun
N-terminal kinase 3 inhibitor through structure-based virtual screening
and in-vitro assay},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {6},
pages = {671--682},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00297-y},
doi = {10.1007/S10822-020-00297-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RajanR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RedzepovicF20,
author = {Izudin Redzepovic and
Boris Furtula},
title = {Predictive potential of eigenvalue-based topological molecular descriptors},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {9},
pages = {975--982},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00320-2},
doi = {10.1007/S10822-020-00320-2},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RedzepovicF20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RiquelmeV20,
author = {Maximiliano Riquelme and
Esteban V{\"{o}}hringer{-}Martinez},
title = {{SAMPL6} Octanol-water partition coefficients from alchemical free
energy calculations with {MBIS} atomic charges},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {4},
pages = {327--334},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00281-6},
doi = {10.1007/S10822-020-00281-6},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RiquelmeV20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RizziJSAGNBPHGC20,
author = {Andrea Rizzi and
Travis Jensen and
David R. Slochower and
Matteo Aldeghi and
Vytautas Gapsys and
Dimitris Ntekoumes and
Stefano Bosisio and
Michail Papadourakis and
Niel M. Henriksen and
Bert L. de Groot and
Zoe Cournia and
Alex Dickson and
Julien Michel and
Michael K. Gilson and
Michael R. Shirts and
David L. Mobley and
John D. Chodera},
title = {The {SAMPL6} SAMPLing challenge: assessing the reliability and efficiency
of binding free energy calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {5},
pages = {601--633},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00290-5},
doi = {10.1007/S10822-020-00290-5},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RizziJSAGNBPHGC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RobinsonGL20,
author = {Matthew C. Robinson and
Robert C. Glen and
Alpha A. Lee},
title = {Validating the validation: reanalyzing a large-scale comparison of
deep learning and machine learning models for bioactivity prediction},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {7},
pages = {717--730},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00274-0},
doi = {10.1007/S10822-019-00274-0},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RobinsonGL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Rodriguez-Perez20,
author = {Raquel Rodr{\'{\i}}guez{-}P{\'{e}}rez and
J{\"{u}}rgen Bajorath},
title = {Interpretation of machine learning models using shapley values: application
to compound potency and multi-target activity predictions},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {10},
pages = {1013--1026},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00314-0},
doi = {10.1007/S10822-020-00314-0},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Rodriguez-Perez20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Sanchez-Marquez20,
author = {Jes{\'{u}}s S{\'{a}}nchez{-}M{\'{a}}rquez and
Victor Garc{\'{\i}}a and
David Zorrilla and
Manuel Fern{\'{a}}ndez},
title = {Software to obtain spatially localized functions from different radial
functions},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {3},
pages = {267--280},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00272-2},
doi = {10.1007/S10822-019-00272-2},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Sanchez-Marquez20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SarfarazML20,
author = {Sara Sarfaraz and
Iqra Muneer and
Haiyan Liu},
title = {Combining fragment docking with graph theory to improve ligand docking
for homology model structures},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {12},
pages = {1237--1259},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00345-7},
doi = {10.1007/S10822-020-00345-7},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SarfarazML20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SasmalEM20,
author = {Sukanya Sasmal and
Lea El{-}Khoury and
David L. Mobley},
title = {{D3R} Grand Challenge 4: ligand similarity and MM-GBSA-based pose
prediction and affinity ranking for {BACE-1} inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {2},
pages = {163--177},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00249-1},
doi = {10.1007/S10822-019-00249-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SasmalEM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Sixto-LopezBC20,
author = {Yudibeth Sixto{-}L{\'{o}}pez and
Martiniano Bello and
Jos{\'{e}} Correa{-}Basurto},
title = {Exploring the inhibitory activity of valproic acid against the {HDAC}
family using an {MMGBSA} approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {8},
pages = {857--878},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00304-2},
doi = {10.1007/S10822-020-00304-2},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Sixto-LopezBC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SoniBJ20,
author = {Anjali Soni and
Ruchika Bhat and
Bhyravabhotla Jayaram},
title = {Improving the binding affinity estimations of protein-ligand complexes
using machine-learning facilitated force field method},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {8},
pages = {817--830},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00305-1},
doi = {10.1007/S10822-020-00305-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SoniBJ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/StroganovNMDGSC20,
author = {Oleg V. Stroganov and
Fedor N. Novikov and
Michael G. Medvedev and
Artem O. Dmitrienko and
Igor S. Gerasimov and
Igor V. Svitanko and
Ghermes G. Chilov},
title = {The role of human in the loop: lessons from {D3R} challenge 4},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {2},
pages = {121--130},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00291-4},
doi = {10.1007/S10822-020-00291-4},
timestamp = {Wed, 06 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/StroganovNMDGSC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/StumpfeHB20,
author = {Dagmar Stumpfe and
Huabin Hu and
J{\"{u}}rgen Bajorath},
title = {Advances in exploring activity cliffs},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {9},
pages = {929--942},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00315-z},
doi = {10.1007/S10822-020-00315-Z},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/StumpfeHB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SunHLZ20,
author = {Zhaoxi Sun and
Qiao{-}Le He and
Xiao Li and
Zhengdan Zhu},
title = {{SAMPL6} host-guest binding affinities and binding poses from spherical-coordinates-biased
simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {5},
pages = {589--600},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00294-1},
doi = {10.1007/S10822-020-00294-1},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SunHLZ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SzwabowskiCSWCB20,
author = {Gregory L. Szwabowski and
Paige N. Castleman and
Chandler K. Sears and
Lee H. Wink and
Judith A. Cole and
Daniel L. Baker and
Abby L. Parrill},
title = {Benchmarking {GPCR} homology model template selection in combination
with de novo loop generation},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {10},
pages = {1027--1044},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00325-x},
doi = {10.1007/S10822-020-00325-X},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SzwabowskiCSWCB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Thiruchittampalam20,
author = {Shalini Thiruchittampalam and
Samantha Weerasinghe},
title = {Plausible compounds drawn from plants as curative agents for neurodegeneration:
An in-silico approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {9},
pages = {1003--1011},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00322-0},
doi = {10.1007/S10822-020-00322-0},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Thiruchittampalam20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TielkerTEGK20,
author = {Nicolas Tielker and
Daniel Tomazic and
Lukas Eberlein and
Stefan G{\"{u}}ssregen and
Stefan M. Kast},
title = {The {SAMPL6} challenge on predicting octanol-water partition coefficients
from {EC-RISM} theory},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {4},
pages = {453--461},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00283-4},
doi = {10.1007/S10822-020-00283-4},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TielkerTEGK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TikhonovLYYZ20,
author = {Denis B. Tikhonov and
Lianyun Lin and
Daniel S. C. Yang and
Zhiguang Yuchi and
Boris S. Zhorov},
title = {Phenylalkylamines in calcium channels: computational analysis of experimental
structures},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {11},
pages = {1157--1169},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00330-0},
doi = {10.1007/S10822-020-00330-0},
timestamp = {Tue, 20 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TikhonovLYYZ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TripathiSTTSSS20,
author = {Manish Kumar Tripathi and
Piyoosh Sharma and
Avanish Tripathi and
Prabhash Nath Tripathi and
Pavan Srivastava and
Ankit Seth and
Sushant Kumar Shrivastava},
title = {Computational exploration and experimental validation to identify
a dual inhibitor of cholinesterase and amyloid-beta for the treatment
of Alzheimer's disease},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {9},
pages = {983--1002},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00318-w},
doi = {10.1007/S10822-020-00318-W},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TripathiSTTSSS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VangalaSPM20,
author = {Radhika Vangala and
Sree Kanth Sivan and
Saikiran Reddy Peddi and
Vijjulatha Manga},
title = {Computational design, synthesis and evaluation of new sulphonamide
derivatives targeting {HIV-1} gp120},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {1},
pages = {39--54},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00258-0},
doi = {10.1007/S10822-019-00258-0},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/VangalaSPM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WangN20,
author = {Bo Wang and
Ho{-}Leung Ng},
title = {Deep neural network affinity model for {BACE} inhibitors in {D3R}
Grand Challenge 4},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {2},
pages = {201--217},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00275-z},
doi = {10.1007/S10822-019-00275-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WangN20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WangR20,
author = {Shuzhe Wang and
Sereina Riniker},
title = {Use of molecular dynamics fingerprints (MDFPs) in {SAMPL6} octanol-water
log {P} blind challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {4},
pages = {393--403},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00252-6},
doi = {10.1007/S10822-019-00252-6},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WangR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WangRZ20,
author = {Huiqun Wang and
Bethany A. Reinecke and
Yan Zhang},
title = {Computational insights into the molecular mechanisms of differentiated
allosteric modulation at the mu opioid receptor by structurally similar
bitopic modulators},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {8},
pages = {879--895},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00309-x},
doi = {10.1007/S10822-020-00309-X},
timestamp = {Tue, 13 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WangRZ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WebelKRNNV20,
author = {Henry E. Webel and
Talia B. Kimber and
Silke Radetzki and
Martin Neuenschwander and
Marc Nazar{\'{e}} and
Andrea Volkamer},
title = {Revealing cytotoxic substructures in molecules using deep learning},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {7},
pages = {731--746},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00310-4},
doi = {10.1007/S10822-020-00310-4},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WebelKRNNV20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/XiaKPT20,
author = {Zhonghua Xia and
Pavel Karpov and
Grzegorz M. Popowicz and
Igor V. Tetko},
title = {Focused Library Generator: case of Mdmx inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {7},
pages = {769--782},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00242-8},
doi = {10.1007/S10822-019-00242-8},
timestamp = {Wed, 15 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/XiaKPT20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/XuZCLSRLZC20,
author = {Xiaoqian Xu and
Li Zhang and
Ying Cai and
Dongxin Liu and
Zhengwen Shang and
Qiuhong Ren and
Qiong Li and
Weidong Zhao and
Yuhua Chen},
title = {Inhibitor discovery for the E. coli meningitis virulence factor IbeA
from homology modeling and virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {1},
pages = {11--25},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00250-8},
doi = {10.1007/S10822-019-00250-8},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/XuZCLSRLZC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YauEL20,
author = {Mei Qian Yau and
Abigail L. Emtage and
Jason S. E. Loo},
title = {Benchmarking the performance of {MM/PBSA} in virtual screening enrichment
using the GPCR-Bench dataset},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {11},
pages = {1133--1145},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00339-5},
doi = {10.1007/S10822-020-00339-5},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/YauEL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YazarO20,
author = {Metin Yazar and
Pemra Ozbek},
title = {Revisiting allostery in CREB-binding protein {(CBP)} using residue-based
interaction energy},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {9},
pages = {965--974},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00316-y},
doi = {10.1007/S10822-020-00316-Y},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YazarO20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YonchevB20,
author = {Dimitar G. Yonchev and
J{\"{u}}rgen Bajorath},
title = {DeepCOMO: from structure-activity relationship diagnostics to generative
molecular design using the compound optimization monitor methodology},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {12},
pages = {1207--1218},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00349-3},
doi = {10.1007/S10822-020-00349-3},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YonchevB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZamoraPGRCL20,
author = {William J. Zamora and
Silvana Pinheiro and
Kilian German and
Clara P{\'{e}}rez{-}R{\`{a}}fols and
Carles Curutchet and
F. Javier Luque},
title = {Prediction of the n-octanol/water partition coefficients in the {SAMPL6}
blind challenge from {MST} continuum solvation calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {4},
pages = {443--451},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00262-4},
doi = {10.1007/S10822-019-00262-4},
timestamp = {Mon, 25 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZamoraPGRCL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Al-ShariAAHAA19,
author = {Nizar A. Al{-}Shar'i and
Qosay A. E. Al{-}Balas and
Rand A. Al{-}Waqfi and
Mohammad A. Hassan and
Amer E. Alkhalifa and
Nehad M. Ayoub},
title = {Discovery of a nanomolar inhibitor of the human glyoxalase-I enzyme
using structure-based poly-pharmacophore modelling and molecular docking},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {9},
pages = {799--815},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00226-8},
doi = {10.1007/S10822-019-00226-8},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Al-ShariAAHAA19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AlbaMD19,
author = {Josephine Alba and
Edoardo Milanetti and
Marco D'Abramo},
title = {On the activation and deactivation pathways of the Lck kinase domain:
a computational study},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {6},
pages = {597--603},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00204-0},
doi = {10.1007/S10822-019-00204-0},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AlbaMD19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AliASA19,
author = {Farman Ali and
Saeed Ahmed and
Zar Nawab Khan Swati and
Shahid Akbar},
title = {{DP-BINDER:} machine learning model for prediction of DNA-binding
proteins by fusing evolutionary and physicochemical information},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {7},
pages = {645--658},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00207-x},
doi = {10.1007/S10822-019-00207-X},
timestamp = {Sun, 30 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AliASA19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BarigyeVC19,
author = {Stephen J. Barigye and
Jos{\'{e}} Manuel Garc{\'{\i}}a de la Vega and
Juan A. Castillo{-}Garit},
title = {Undersampling: case studies of flaviviral inhibitory activities},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {11},
pages = {997--1008},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00255-3},
doi = {10.1007/S10822-019-00255-3},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BarigyeVC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BustamanteOAM19,
author = {Christian Bustamante and
Rodrigo Ochoa and
Claudia Asela and
Carlos Muskus},
title = {Repurposing of known drugs for leishmaniasis treatment using bioinformatic
predictions, in vitro validations and pharmacokinetic simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {9},
pages = {845--854},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00230-y},
doi = {10.1007/S10822-019-00230-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BustamanteOAM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Cardoso-SilvaPT19,
author = {Jonathan Cardoso{-}Silva and
Lazaros G. Papageorgiou and
Sophia Tsoka},
title = {Network-based piecewise linear regression for {QSAR} modelling},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {9},
pages = {831--844},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00228-6},
doi = {10.1007/S10822-019-00228-6},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Cardoso-SilvaPT19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChaputSEI19,
author = {Ludovic Chaput and
Edithe Selwa and
Eddy Elis{\'{e}}e and
Bogdan I. Iorga},
title = {Blinded evaluation of cathepsin {S} inhibitors from the {D3RGC3} dataset
using molecular docking and free energy calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {1},
pages = {93--103},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0161-7},
doi = {10.1007/S10822-018-0161-7},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChaputSEI19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChellapandiPP19,
author = {P. Chellapandi and
R. Prathiviraj and
A. Prisilla},
title = {Deciphering structure, function and mechanism of Plasmodium IspD homologs
from their evolutionary imprints},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {4},
pages = {419--436},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00191-2},
doi = {10.1007/S10822-019-00191-2},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChellapandiPP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChenWGY019,
author = {Han Chen and
Yan Wang and
Zheng Gao and
Wen Yang and
Jian Gao},
title = {Assessing the performance of three resveratrol in binding with {SIRT1}
by molecular dynamics simulation and {MM/GBSA} methods: the weakest
binding of resveratrol 3 to {SIRT1} triggers a possibility of dissociation
from its binding site},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {4},
pages = {437--446},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00193-0},
doi = {10.1007/S10822-019-00193-0},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChenWGY019.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CiancettaRLJ19,
author = {Antonella Ciancetta and
Priscila Rubio and
David I. Lieberman and
Kenneth A. Jacobson},
title = {A\({}_{\mbox{3}}\) adenosine receptor activation mechanisms: molecular
dynamics analysis of inactive, active, and fully active states},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {11},
pages = {983--996},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00246-4},
doi = {10.1007/S10822-019-00246-4},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CiancettaRLJ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ClevesJJ19,
author = {Ann E. Cleves and
Stephen R. Johnson and
Ajay N. Jain},
title = {Electrostatic-field and surface-shape similarity for virtual screening
and pose prediction},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {10},
pages = {865--886},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00236-6},
doi = {10.1007/S10822-019-00236-6},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ClevesJJ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CrucianiMVLGS19,
author = {Gabriele Cruciani and
Yvonne C. Martin and
Andy Vinter and
Richard Lewis and
Federico Gago and
Terry R. Stouch},
title = {How computational chemistry develops: a tribute to Peter Goodford},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {8},
pages = {699--703},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00217-9},
doi = {10.1007/S10822-019-00217-9},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CrucianiMVLGS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Dauber-Osguthorpe19,
author = {Pnina Dauber{-}Osguthorpe and
Arnold T. Hagler},
title = {Biomolecular force fields: where have we been, where are we now, where
do we need to go and how do we get there?},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {2},
pages = {133--203},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0111-4},
doi = {10.1007/S10822-018-0111-4},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Dauber-Osguthorpe19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/El-KhourySSEBAS19,
author = {Lea El{-}Khoury and
Diogo Santos{-}Martins and
Sukanya Sasmal and
J{\'{e}}r{\^{o}}me Eberhardt and
Giulia Bianco and
Francesca Alessandra Ambrosio and
Leonardo Solis{-}Vasquez and
Andreas Koch and
Stefano Forli and
David L. Mobley},
title = {Comparison of affinity ranking using AutoDock-GPU and {MM-GBSA} scores
for {BACE-1} inhibitors in the {D3R} Grand Challenge 4},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {12},
pages = {1011--1020},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00240-w},
doi = {10.1007/S10822-019-00240-W},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/El-KhourySSEBAS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/EliseeGMCSGI19,
author = {Eddy Elis{\'{e}}e and
Vytautas Gapsys and
Nawel Mele and
Ludovic Chaput and
Edithe Selwa and
Bert L. de Groot and
Bogdan I. Iorga},
title = {Performance evaluation of molecular docking and free energy calculations
protocols using the {D3R} Grand Challenge 4 dataset},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {12},
pages = {1031--1043},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00232-w},
doi = {10.1007/S10822-019-00232-W},
timestamp = {Tue, 16 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/EliseeGMCSGI19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FusaniC19,
author = {Lucia Fusani and
{\'{A}}lvaro Cort{\'{e}}s Cabrera},
title = {Active learning strategies with {COMBINE} analysis: new tricks for
an old dog},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {2},
pages = {287--294},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0181-3},
doi = {10.1007/S10822-018-0181-3},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/FusaniC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GaiebPCYSWLNBAM19,
author = {Zied Gaieb and
Conor D. Parks and
Michael Chiu and
Huanwang Yang and
Chenghua Shao and
W. Patrick Walters and
Millard H. Lambert and
Neysa Nevins and
Scott D. Bembenek and
Michael K. Ameriks and
Tara Mirzadegan and
Stephen K. Burley and
Rommie E. Amaro and
Michael K. Gilson},
title = {{D3R} Grand Challenge 3: blind prediction of protein-ligand poses
and affinity rankings},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {1},
pages = {1--18},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0180-4},
doi = {10.1007/S10822-018-0180-4},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GaiebPCYSWLNBAM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GeBHXW19,
author = {Haixia Ge and
Yuemin Bian and
Xibing He and
Xiang{-}Qun Xie and
Junmei Wang},
title = {Significantly different effects of tetrahydroberberrubine enantiomers
on dopamine {D1/D2} receptors revealed by experimental study and integrated
in silico simulation},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {4},
pages = {447--459},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00194-z},
doi = {10.1007/S10822-019-00194-Z},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GeBHXW19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Gilson19,
author = {Michael K. Gilson},
title = {This issue: Drug Design Data Resource Grand Challenge 4, first of
two issues},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {12},
pages = {1009},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00265-1},
doi = {10.1007/S10822-019-00265-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Gilson19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Hagler19,
author = {Arnold T. Hagler},
title = {Force field development phase {II:} Relaxation of physics-based criteria...
or inclusion of more rigorous physics into the representation of molecular
energetics},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {2},
pages = {205--264},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0134-x},
doi = {10.1007/S10822-018-0134-X},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Hagler19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HameedMHASA19,
author = {Asima Hameed and
Sara Masood and
Aamir Hameed and
Ejaz Ahmed and
Ahsan Sharif and
Muhammad Imran Abdullah},
title = {Anti-malarial, cytotoxicity and molecular docking studies of quinolinyl
chalcones as potential anti-malarial agent},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {7},
pages = {677--688},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00210-2},
doi = {10.1007/S10822-019-00210-2},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HameedMHASA19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HanS19,
author = {Min Han and
Dongdong Sun},
title = {Rational creation and systematic analysis of cervical cancer kinase-inhibitor
binding profile},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {7},
pages = {689--698},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00211-1},
doi = {10.1007/S10822-019-00211-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HanS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HeMJXW19,
author = {Xibing He and
Viet Hoang Man and
Beihong Ji and
Xiang{-}Qun Xie and
Junmei Wang},
title = {Calculate protein-ligand binding affinities with the extended linear
interaction energy method: application on the Cathepsin {S} set in
the {D3R} Grand Challenge 3},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {1},
pages = {105--117},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0162-6},
doi = {10.1007/S10822-018-0162-6},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/HeMJXW19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HingeBRWK19,
author = {Vijaya Kumar Hinge and
Nikolay Blinov and
Dipankar Roy and
David S. Wishart and
Andriy Kovalenko},
title = {The role of hydration effects in 5-fluorouridine binding to {SOD1:}
insight from a new 3D-RISM-KH based protocol for including structural
water in docking simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {10},
pages = {913--926},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00239-3},
doi = {10.1007/S10822-019-00239-3},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HingeBRWK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HingeRK19,
author = {Vijaya Kumar Hinge and
Dipankar Roy and
Andriy Kovalenko},
title = {Predicting skin permeability using the 3D-RISM-KH theory based solvation
energy descriptors for a diverse class of compounds},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {6},
pages = {605--611},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00205-z},
doi = {10.1007/S10822-019-00205-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HingeRK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HingeRK19a,
author = {Vijaya Kumar Hinge and
Dipankar Roy and
Andriy Kovalenko},
title = {Prediction of P-glycoprotein inhibitors with machine learning classification
models and 3D-RISM-KH theory based solvation energy descriptors},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {11},
pages = {965--971},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00253-5},
doi = {10.1007/S10822-019-00253-5},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HingeRK19a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HuZLLTLBHS19,
author = {Xin Hu and
Ya{-}Qin Zhang and
Olivia W. Lee and
Li Liu and
Manshu Tang and
Kent Lai and
Matthew B. Boxer and
Matthew D. Hall and
Min Shen},
title = {Discovery of novel inhibitors of human galactokinase by virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {4},
pages = {405--417},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00190-3},
doi = {10.1007/S10822-019-00190-3},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/HuZLLTLBHS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/IgnatovLASPKKGK19,
author = {Mikhail Ignatov and
Cong Liu and
Andrey Alekseenko and
Zhuyezi Sun and
Dzmitry Padhorny and
Sergei Kotelnikov and
Andrey M. Kazennov and
Ivan Grebenkin and
Yaroslav Kholodov and
Istvan Kolosvari and
Alberto P{\'{e}}rez and
Ken A. Dill and
Dima Kozakov},
title = {Monte Carlo on the manifold and {MD} refinement for binding pose prediction
of protein-ligand complexes: 2017 {D3R} Grand Challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {1},
pages = {119--127},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0176-0},
doi = {10.1007/S10822-018-0176-0},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/IgnatovLASPKKGK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JainCGWLSR19,
author = {Ajay N. Jain and
Ann E. Cleves and
Qi Gao and
Xiao Wang and
Yizhou Liu and
Edward C. Sherer and
Mikhail Y. Reibarkh},
title = {Complex macrocycle exploration: parallel, heuristic, and constraint-based
conformer generation using ForceGen},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {6},
pages = {531--558},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00203-1},
doi = {10.1007/S10822-019-00203-1},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JainCGWLSR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JiangGCSWZZ19,
author = {Cheng{-}Shi Jiang and
Yong{-}Xi Ge and
Zhi{-}Qiang Cheng and
Jia{-}Li Song and
Yin{-}Yin Wang and
Kongkai Zhu and
Hua Zhang},
title = {Discovery of new multifunctional selective acetylcholinesterase inhibitors:
structure-based virtual screening and biological evaluation},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {5},
pages = {521--530},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00202-2},
doi = {10.1007/S10822-019-00202-2},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/JiangGCSWZZ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KanaB19,
author = {Omar Kana and
Michal Brylinski},
title = {Elucidating the druggability of the human proteome with eFindSite},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {5},
pages = {509--519},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00197-w},
doi = {10.1007/S10822-019-00197-W},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KanaB19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KoukosXB19,
author = {Panagiotis I. Koukos and
Li C. Xue and
Alexandre M. J. J. Bonvin},
title = {Protein-ligand pose and affinity prediction: Lessons from {D3R} Grand
Challenge 3},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {1},
pages = {83--91},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0148-4},
doi = {10.1007/S10822-018-0148-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KoukosXB19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KrebsES19,
author = {Fanny S. Krebs and
Jeremy Esque and
Roland H. Stote},
title = {A computational study of the molecular basis of antibiotic resistance
in a {DXR} mutant},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {10},
pages = {927--940},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00229-5},
doi = {10.1007/S10822-019-00229-5},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KrebsES19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KrishnaZRGS19,
author = {Vagolu Siva Krishna and
Shan Zheng and
Estharla Madhu Rekha and
Luke W. Guddat and
Dharmarajan Sriram},
title = {Discovery and evaluation of novel Mycobacterium tuberculosis ketol-acid
reductoisomerase inhibitors as therapeutic drug leads},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {3},
pages = {357--366},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00184-1},
doi = {10.1007/S10822-019-00184-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KrishnaZRGS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KumarZ19,
author = {Ashutosh Kumar and
Kam Y. J. Zhang},
title = {Shape similarity guided pose prediction: lessons from {D3R} Grand
Challenge 3},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {1},
pages = {47--59},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0142-x},
doi = {10.1007/S10822-018-0142-X},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KumarZ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KumarZ19a,
author = {Ashutosh Kumar and
Kam Y. J. Zhang},
title = {Improving ligand 3D shape similarity-based pose prediction with a
continuum solvent model},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {12},
pages = {1045--1055},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00220-0},
doi = {10.1007/S10822-019-00220-0},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KumarZ19a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LamAT19,
author = {Polo Chun{-}Hung Lam and
Ruben Abagyan and
Maxim Totrov},
title = {Hybrid receptor structure/ligand-based docking and activity prediction
in {ICM:} development and evaluation in {D3R} Grand Challenge 3},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {1},
pages = {35--46},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0139-5},
doi = {10.1007/S10822-018-0139-5},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LamAT19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LamAT19a,
author = {Polo Chun{-}Hung Lam and
Ruben Abagyan and
Maxim Totrov},
title = {Macrocycle modeling in {ICM:} benchmarking and evaluation in {D3R}
Grand Challenge 4},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {12},
pages = {1057--1069},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00225-9},
doi = {10.1007/S10822-019-00225-9},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LamAT19a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LinHMBV19,
author = {Arkadii I. Lin and
Dragos Horvath and
Gilles Marcou and
Bernd Beck and
Alexandre Varnek},
title = {Multi-task generative topographic mapping in virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {3},
pages = {331--343},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00188-x},
doi = {10.1007/S10822-019-00188-X},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LinHMBV19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuJHC19,
author = {Guangpu Liu and
Yang Jiao and
Chunxi Huang and
Ping Chang},
title = {Identification of novel and potent small-molecule inhibitors of tubulin
with antitumor activities by virtual screening and biological evaluations},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {7},
pages = {659--664},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00206-y},
doi = {10.1007/S10822-019-00206-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiuJHC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuJZLLMW19,
author = {Wen{-}Shan Liu and
Wen{-}Yan Jin and
Liang Zhou and
Xing{-}Hua Lu and
Wei{-}Ya Li and
Ying Ma and
Run{-}Ling Wang},
title = {Structure based design of selective {SHP2} inhibitors by De novo design,
synthesis and biological evaluation},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {8},
pages = {759--774},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00213-z},
doi = {10.1007/S10822-019-00213-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiuJZLLMW19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuK19,
author = {Kai Liu and
Hironori Kokubo},
title = {Uncovering abnormal changes in logP after fluorination using molecular
dynamics simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {3},
pages = {345--356},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0183-1},
doi = {10.1007/S10822-018-0183-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiuK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MacariTP19,
author = {Gabriele Macari and
Daniele Toti and
Fabio Polticelli},
title = {Computational methods and tools for binding site recognition between
proteins and small molecules: from classical geometrical approaches
to modern machine learning strategies},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {10},
pages = {887--903},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00235-7},
doi = {10.1007/S10822-019-00235-7},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MacariTP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MiljkovicVB19,
author = {Filip Miljkovic and
Martin Vogt and
J{\"{u}}rgen Bajorath},
title = {Systematic computational identification of promiscuity cliff pathways
formed by inhibitors of the human kinome},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {6},
pages = {559--572},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00198-9},
doi = {10.1007/S10822-019-00198-9},
timestamp = {Mon, 30 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/MiljkovicVB19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MiyaoJBF19,
author = {Tomoyuki Miyao and
Swarit Jasial and
J{\"{u}}rgen Bajorath and
Kimito Funatsu},
title = {Evaluation of different virtual screening strategies on the basis
of compound sets with characteristic core distributions and dissimilarity
relationships},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {8},
pages = {729--743},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00218-8},
doi = {10.1007/S10822-019-00218-8},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MiyaoJBF19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MomanGP19,
author = {Edelmiro Moman and
Maria A. Grishina and
Vladimir Potemkin},
title = {Nonparametric chemical descriptors for the calculation of ligand-biopolymer
affinities with machine-learning scoring functions},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {11},
pages = {943--953},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00248-2},
doi = {10.1007/S10822-019-00248-2},
timestamp = {Wed, 12 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MomanGP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NguyenCWWCW19,
author = {Duc Duy Nguyen and
Zixuan Cang and
Kedi Wu and
Menglun Wang and
Yin Cao and
Guo{-}Wei Wei},
title = {Mathematical deep learning for pose and binding affinity prediction
and ranking in {D3R} Grand Challenges},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {1},
pages = {71--82},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0146-6},
doi = {10.1007/S10822-018-0146-6},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NguyenCWWCW19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NguyenJR19,
author = {Minh Khoa Nguyen and
L{\'{e}}onard Jaillet and
St{\'{e}}phane Redon},
title = {{ART-RRT:} As-Rigid-As-Possible search for protein conformational
transition paths},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {8},
pages = {705--727},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00216-w},
doi = {10.1007/S10822-019-00216-W},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NguyenJR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NittingerGEDMYK19,
author = {Eva Nittinger and
Paul Gibbons and
Charles Eigenbrot and
Doug R. Davies and
Brigitte Maurer and
Christine L. Yu and
James R. Kiefer and
Andreas Kuglstatter and
Jeremy Murray and
Daniel F. Ortwine and
Yong Tang and
Vickie Tsui},
title = {Water molecules in protein-ligand interfaces. Evaluation of software
tools and {SAR} comparison},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {3},
pages = {307--330},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00187-y},
doi = {10.1007/S10822-019-00187-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NittingerGEDMYK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OrgovanFK19,
author = {Zolt{\'{a}}n Orgov{\'{a}}n and
Gy{\"{o}}rgy G. Ferenczy and
Gy{\"{o}}rgy M. Keser{\"{u}}},
title = {The role of water and protein flexibility in the structure-based virtual
screening of allosteric {GPCR} modulators: an mGlu5 receptor case
study},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {9},
pages = {787--797},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00224-w},
doi = {10.1007/S10822-019-00224-W},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OrgovanFK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PretoG19,
author = {Jordane Preto and
Francesco Gentile},
title = {Assessing and improving the performance of consensus docking strategies
using the DockBox package},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {9},
pages = {817--829},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00227-7},
doi = {10.1007/S10822-019-00227-7},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PretoG19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Ragno19,
author = {Rino Ragno},
title = {www.3d-qsar.com: a web portal that brings 3-D {QSAR} to all electronic
devices - the Py-CoMFA web application as tool to build models from
pre-aligned datasets},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {9},
pages = {855--864},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00231-x},
doi = {10.1007/S10822-019-00231-X},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Ragno19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RazaRKWMA19,
author = {Saad Raza and
Kara E. Ranaghan and
Marc van der Kamp and
Christopher J. Woods and
Adrian J. Mulholland and
Syed Sikander Azam},
title = {Visualizing protein-ligand binding with chemical energy-wise decomposition
{(CHEWD):} application to ligand binding in the kallikrein-8 {S1}
Site},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {5},
pages = {461--475},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00200-4},
doi = {10.1007/S10822-019-00200-4},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RazaRKWMA19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RedijMLHL19,
author = {Tejashree Redij and
Jian Ma and
Zhiyu Li and
Xianxin Hua and
Zhijun Li},
title = {Discovery of a potential positive allosteric modulator of glucagon-like
peptide 1 receptor through virtual screening and experimental study},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {11},
pages = {973--981},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00254-4},
doi = {10.1007/S10822-019-00254-4},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RedijMLHL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RekerL19,
author = {Daniel Reker and
Richard A. Lewis},
title = {Advanced Editorial to announce a {JCAMD} Special Issue on Artificial
Intelligence and Machine Learning},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {11},
pages = {941},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00264-2},
doi = {10.1007/S10822-019-00264-2},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/RekerL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RotermanDGBK19,
author = {Irena Roterman and
Dawid Dulak and
Malgorzata Gadzala and
Mateusz Banach and
Leszek Konieczny},
title = {Structural analysis of the A{\(\beta\)}(11-42) amyloid fibril based
on hydrophobicity distribution},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {7},
pages = {665--675},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00209-9},
doi = {10.1007/S10822-019-00209-9},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RotermanDGBK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RoyK19,
author = {Dipankar Roy and
Andriy Kovalenko},
title = {Application of the 3D-RISM-KH molecular solvation theory for {DMSO}
as solvent},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {10},
pages = {905--912},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00238-4},
doi = {10.1007/S10822-019-00238-4},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RoyK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Sanchez-MurciaM19,
author = {Pedro A. S{\'{a}}nchez{-}Murcia and
Alberto Mills and
{\'{A}}lvaro Cort{\'{e}}s Cabrera and
Federico Gago},
title = {Unravelling the covalent binding of zampanolide and taccalonolide
{AJ} to a minimalist representation of a human microtubule},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {7},
pages = {627--644},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00208-w},
doi = {10.1007/S10822-019-00208-W},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Sanchez-MurciaM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Santos-MartinsE19,
author = {Diogo Santos{-}Martins and
J{\'{e}}r{\^{o}}me Eberhardt and
Giulia Bianco and
Leonardo Solis{-}Vasquez and
Francesca Alessandra Ambrosio and
Andreas Koch and
Stefano Forli},
title = {{D3R} Grand Challenge 4: prospective pose prediction of {BACE1} ligands
with AutoDock-GPU},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {12},
pages = {1071--1081},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00241-9},
doi = {10.1007/S10822-019-00241-9},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Santos-MartinsE19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Sekhar19,
author = {Pagadala Nataraj Sekhar},
title = {{AZT} acts as an anti-influenza nucleotide triphosphate targeting
the catalytic site of {A/PR/8/34/H1N1} {RNA} dependent {RNA} polymerase},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {4},
pages = {387--404},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00189-w},
doi = {10.1007/S10822-019-00189-W},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Sekhar19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ShinK19,
author = {Woong{-}Hee Shin and
Daisuke Kihara},
title = {Predicting binding poses and affinity ranking in {D3R} Grand Challenge
using PL-PatchSurfer2.0},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {12},
pages = {1083--1094},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00222-y},
doi = {10.1007/S10822-019-00222-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ShinK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SimeonJCG19,
author = {Saw Simeon and
Nathjanan Jongkon and
Warot Chotpatiwetchkul and
Matthew Paul Gleeson},
title = {Insights into the {EGFR} {SAR} of N-phenylquinazolin-4-amine-derivatives
using quantum mechanical pairwise-interaction energies},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {8},
pages = {745--757},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00221-z},
doi = {10.1007/S10822-019-00221-Z},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SimeonJCG19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SolerWS19,
author = {Daniel Soler and
Yvonne Westermaier and
Robert Soliva},
title = {Extensive benchmark of rDock as a peptide-protein docking tool},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {7},
pages = {613--626},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00212-0},
doi = {10.1007/S10822-019-00212-0},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SolerWS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SoongCLC19,
author = {Jia Xin Soong and
Soo Khim Chan and
Theam Soon Lim and
Yee{-}Siew Choong},
title = {Optimisation of human {VH} domain antibodies specific to Mycobacterium
tuberculosis heat shock protein {(HSP16.3)}},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {3},
pages = {375--385},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00186-z},
doi = {10.1007/S10822-019-00186-Z},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SoongCLC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SpyrakisBQLBDBC19,
author = {Francesca Spyrakis and
Pierangelo Bellio and
Antonio Quotadamo and
Pasquale Linciano and
Paolo Benedetti and
Giulia D'Arrigo and
Massimo Baroni and
Laura Cendron and
Giuseppe Celenza and
Donatella Tondi},
title = {First virtual screening and experimental validation of inhibitors
targeting {GES-5} carbapenemase},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {2},
pages = {295--305},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0182-2},
doi = {10.1007/S10822-018-0182-2},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SpyrakisBQLBDBC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Stouch19,
author = {Terry Richard Stouch},
title = {The backbone of our chemical computations},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {2},
pages = {129--131},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00192-1},
doi = {10.1007/S10822-019-00192-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Stouch19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SunseriKFK19,
author = {Jocelyn Sunseri and
Jonathan E. King and
Paul G. Francoeur and
David Ryan Koes},
title = {Convolutional neural network scoring and minimization in the {D3R}
2017 community challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {1},
pages = {19--34},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0133-y},
doi = {10.1007/S10822-018-0133-Y},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SunseriKFK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Triantaphyllopoulos19,
author = {Kostas A. Triantaphyllopoulos and
Fotis A. Baltoumas and
Stavros J. Hamodrakas},
title = {Structural characterization and molecular dynamics simulations of
the caprine and bovine solute carrier family 11 {A1} {(SLC11A1)}},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {2},
pages = {265--285},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0179-x},
doi = {10.1007/S10822-018-0179-X},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Triantaphyllopoulos19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VolynetsSRBKVYT19,
author = {Galyna P. Volynets and
Sergiy A. Starosyla and
Mariia Yu. Rybak and
Volodymyr G. Bdzhola and
Oksana P. Kovalenko and
Vasyl S. Vdovin and
Sergiy M. Yarmoluk and
Michail A. Tukalo},
title = {Dual-targeted hit identification using pharmacophore screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {11},
pages = {955--964},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00245-5},
doi = {10.1007/S10822-019-00245-5},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/VolynetsSRBKVYT19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VuMAM19,
author = {Oanh Vu and
Jeffrey L. Mendenhall and
Doaa Altarawy and
Jens Meiler},
title = {{BCL:} : Mol2D - a robust atom environment descriptor for {QSAR} modeling
and lead optimization},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {5},
pages = {477--486},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00199-8},
doi = {10.1007/S10822-019-00199-8},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VuMAM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WinkBCP19,
author = {Lee H. Wink and
Daniel L. Baker and
Judith A. Cole and
Abby L. Parrill},
title = {A benchmark study of loop modeling methods applied to {G} protein-coupled
receptors},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {6},
pages = {573--595},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00196-x},
doi = {10.1007/S10822-019-00196-X},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WinkBCP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/XieM19,
author = {Bing Xie and
David D. L. Minh},
title = {Alchemical Grid Dock (AlGDock) calculations in the {D3R} Grand Challenge
3 - Binding free energies between flexible ligands and rigid receptors},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {1},
pages = {61--69},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0143-9},
doi = {10.1007/S10822-018-0143-9},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/XieM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/XuMDZ19,
author = {Xianjin Xu and
Zhiwei Ma and
Rui Duan and
Xiaoqin Zou},
title = {Predicting protein-ligand binding modes for {CELPP} and {GC3:} workflows
and insight},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {3},
pages = {367--374},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00185-0},
doi = {10.1007/S10822-019-00185-0},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/XuMDZ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YamasakiAYHF19,
author = {Satoshi Yamasaki and
Takayuki Amemiya and
Yukimitsu Yabuki and
Katsuhisa Horimoto and
Kazuhiko Fukui},
title = {ToGo-WF: prediction of {RNA} tertiary structures and RNA-RNA/protein
interactions using the {KNIME} workflow},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {5},
pages = {497--507},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00195-y},
doi = {10.1007/S10822-019-00195-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YamasakiAYHF19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YangLYZ19,
author = {Yuwei Yang and
Jianing Lu and
Chao Yang and
Yingkai Zhang},
title = {Exploring fragment-based target-specific ranking protocol with machine
learning on cathepsin {S}},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {12},
pages = {1095--1105},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00247-3},
doi = {10.1007/S10822-019-00247-3},
timestamp = {Thu, 05 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YangLYZ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YauECDL19,
author = {Mei Qian Yau and
Abigail L. Emtage and
Nathaniel J. Y. Chan and
Stephen W. Doughty and
Jason S. E. Loo},
title = {Evaluating the performance of {MM/PBSA} for binding affinity prediction
using class {A} {GPCR} crystal structures},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {5},
pages = {487--496},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00201-3},
doi = {10.1007/S10822-019-00201-3},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/YauECDL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhuSTYLZD19,
author = {Kongkai Zhu and
Jingwei Shao and
Hongrui Tao and
Xue Yan and
Cheng Luo and
Hua Zhang and
Wenhu Duan},
title = {Rational Design, synthesis and biological evaluation of novel triazole
derivatives as potent and selective {PRMT5} inhibitors with antitumor
activity},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {8},
pages = {775--785},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00214-y},
doi = {10.1007/S10822-019-00214-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZhuSTYLZD19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZouTS19,
author = {Junjie Zou and
Chuan Tian and
Carlos Simmerling},
title = {Blinded prediction of protein-ligand binding affinity using Amber
thermodynamic integration for the 2018 {D3R} grand challenge 4},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {12},
pages = {1021--1029},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00223-x},
doi = {10.1007/S10822-019-00223-X},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZouTS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AgrafiotisHJRST18,
author = {Dimitris K. Agrafiotis and
M. Katharine Holloway and
Scott A. Johnson and
Charles H. Reynolds and
Terry R. Stouch and
Alexander Tropsha and
Chris L. Waller},
title = {Chemistry, information and Frank: a tribute to Frank Brown},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {7},
pages = {723--729},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0135-9},
doi = {10.1007/S10822-018-0135-9},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AgrafiotisHJRST18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AthanasiouVDC18,
author = {Christina Athanasiou and
Sofia Vasilakaki and
Dimitris Dellis and
Zoe Cournia},
title = {Using physics-based pose predictions and free energy perturbation
calculations to predict binding poses and relative binding affinities
for {FXR} ligands in the {D3R} Grand Challenge 2},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {21--44},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0075-9},
doi = {10.1007/S10822-017-0075-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AthanasiouVDC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BannanMS18,
author = {Caitlin C. Bannan and
David L. Mobley and
A. Geoffrey Skillman},
title = {{SAMPL6} challenge results from \({}_{\mbox{a}}\) predictions based
on a general Gaussian process model},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1165--117},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0169-z},
doi = {10.1007/S10822-018-0169-Z},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/BannanMS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BaumgartnerE18,
author = {Matthew P. Baumgartner and
David A. Evans},
title = {Lessons learned in induced fit docking and metadynamics in the Drug
Design Data Resource Grand Challenge 2},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {45--58},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0081-y},
doi = {10.1007/S10822-017-0081-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BaumgartnerE18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BelkinKV18,
author = {Saveliy Belkin and
Petras J. Kundrotas and
Ilya A. Vakser},
title = {Inhibition of protein interactions: co-crystalized protein-protein
interfaces are nearly as good as holo proteins in rigid-body ligand
docking},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {7},
pages = {769--779},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0124-z},
doi = {10.1007/S10822-018-0124-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BelkinKV18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BhakatAS18,
author = {Soumendranath Bhakat and
Emil {\AA}berg and
P{\"{a}}r S{\"{o}}derhjelm},
title = {Prediction of binding poses to {FXR} using multi-targeted docking
combined with molecular dynamics and enhanced sampling},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {59--73},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0074-x},
doi = {10.1007/S10822-017-0074-X},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BhakatAS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CaballeroMN18,
author = {Julio Caballero and
Alejandro Morales{-}Bayuelo and
Carlos Navarro{-}Retamal},
title = {Mycobacterium tuberculosis serine/threonine protein kinases: structural
information for the design of their specific ATP-competitive inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {12},
pages = {1315--1336},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0173-3},
doi = {10.1007/S10822-018-0173-3},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CaballeroMN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CaldararuOIWR18,
author = {Octav Caldararu and
Martin A. Olsson and
Majda Misini Ignjatovic and
Meiting Wang and
Ulf Ryde},
title = {Binding free energies in the {SAMPL6} octa-acid host-guest challenge
calculated with {MM} and {QM} methods},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1027--1046},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0158-2},
doi = {10.1007/S10822-018-0158-2},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CaldararuOIWR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CardamoneFD18,
author = {Francesca Cardamone and
Mattia Falconi and
Alessandro Desideri},
title = {Molecular dynamics characterization of the {SAMHD1} Aicardi-Gouti{\`{e}}res
Arg145Gln mutant: structural determinants for the impaired tetramerization},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {5},
pages = {623--632},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0115-0},
doi = {10.1007/S10822-018-0115-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CardamoneFD18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Carrillo-TrippA18,
author = {Mauricio Carrillo{-}Tripp and
Leonardo Alvarez{-}Rivera and
Omar Israel Lara{-}Ram{\'{\i}}rez and
Francisco Javier Becerra{-}Toledo and
Adan Vega{-}Ram{\'{\i}}rez and
Emmanuel Quijas{-}Valades and
Eduardo Gonz{\'{a}}lez{-}Zavala and
Julio Cesar Gonz{\'{a}}lez{-}V{\'{a}}zquez and
Javier Garc{\'{\i}}a{-}Vieyra and
Nelly Beatriz Santoyo{-}Rivera and
Sergio V{\'{\i}}ctor Chapa Vergara and
Amilcar Meneses Viveros},
title = {HTMoL: full-stack solution for remote access, visualization, and analysis
of molecular dynamics trajectory data},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {8},
pages = {869--876},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0141-y},
doi = {10.1007/S10822-018-0141-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Carrillo-TrippA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChenLPLP18,
author = {Jie Chen and
Xiao Lin and
Kyoung Jin Park and
Kang Ro Lee and
Hyun{-}Ju Park},
title = {Identification of protoberberine alkaloids as novel histone methyltransferase
G9a inhibitors by structure-based virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {9},
pages = {917--928},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0156-4},
doi = {10.1007/S10822-018-0156-4},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChenLPLP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CholkoCTC18,
author = {Timothy Cholko and
Wei Chen and
Zhiye Tang and
Chia{-}en A. Chang},
title = {A molecular dynamics investigation of CDK8/CycC and ligand binding:
conformational flexibility and implication in drug discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {6},
pages = {671--685},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0120-3},
doi = {10.1007/S10822-018-0120-3},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CholkoCTC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ClevesJ18,
author = {Ann E. Cleves and
Ajay N. Jain},
title = {Quantitative surface field analysis: learning causal models to predict
ligand binding affinity and pose},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {7},
pages = {731--757},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0126-x},
doi = {10.1007/S10822-018-0126-X},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ClevesJ18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Della-LongaA18,
author = {Stefano Della{-}Longa and
Alessandro Arcovito},
title = {"In silico" study of the binding of two novel antagonists to the nociceptin
receptor},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {2},
pages = {385--400},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0095-5},
doi = {10.1007/S10822-017-0095-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Della-LongaA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DingHVCB18,
author = {Xinqiang Ding and
Ryan L. Hayes and
Jonah Z. Vilseck and
Murchtricia K. Charles and
Charles L. Brooks III},
title = {{CDOCKER} and {\(\lambda\)}-dynamics for prospective prediction in
{D3R} Grand Challenge 2},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {89--102},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0050-5},
doi = {10.1007/S10822-017-0050-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DingHVCB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DixonLD18,
author = {Tom Dixon and
Samuel D. Lotz and
Alex Dickson},
title = {Predicting ligand binding affinity using on- and off-rates for the
{SAMPL6} SAMPLing challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1001--1012},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0149-3},
doi = {10.1007/S10822-018-0149-3},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DixonLD18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DuanXZ18,
author = {Rui Duan and
Xianjin Xu and
Xiaoqin Zou},
title = {Lessons learned from participating in {D3R} 2016 Grand Challenge 2:
compounds targeting the farnesoid {X} receptor},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {103--111},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0082-x},
doi = {10.1007/S10822-017-0082-X},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DuanXZ18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/EkenPDJW18,
author = {Yigitcan Eken and
Prajay Patel and
Thomas D{\'{\i}}az and
Michael R. Jones and
Angela K. Wilson},
title = {{SAMPL6} host-guest challenge: binding free energies via a multistep
approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1097--1115},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0159-1},
doi = {10.1007/S10822-018-0159-1},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/EkenPDJW18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FraderaVHWWFACS18,
author = {Xavier Fradera and
Andreas Verras and
Yuan Hu and
Deping Wang and
Hongwu Wang and
James I. Fells and
Kira A. Armacost and
Alejandro Crespo and
Brad Sherborne and
Huijun Wang and
Zhengwei Peng and
Ying{-}Duo Gao},
title = {Performance of multiple docking and refinement methods in the pose
prediction {D3R} prospective Grand Challenge 2016},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {113--127},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0053-2},
doi = {10.1007/S10822-017-0053-2},
timestamp = {Sat, 30 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/FraderaVHWWFACS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GaiebLGCYSFWKRB18,
author = {Zied Gaieb and
Shuai Liu and
Symon Gathiaka and
Michael Chiu and
Huanwang Yang and
Chenghua Shao and
Victoria A. Feher and
W. Patrick Walters and
Bernd Kuhn and
Markus G. Rudolph and
Stephen K. Burley and
Michael K. Gilson and
Rommie E. Amaro},
title = {{D3R} Grand Challenge 2: blind prediction of protein-ligand poses,
affinity rankings, and relative binding free energies},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {1--20},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0088-4},
doi = {10.1007/S10822-017-0088-4},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GaiebLGCYSFWKRB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GaoHCWAFFWWSVP18,
author = {Ying{-}Duo Gao and
Yuan Hu and
Alejandro Crespo and
Deping Wang and
Kira A. Armacost and
James I. Fells and
Xavier Fradera and
Hongwu Wang and
Huijun Wang and
Brad Sherborne and
Andreas Verras and
Zhengwei Peng},
title = {Workflows and performances in the ranking prediction of 2016 {D3R}
Grand Challenge 2: lessons learned from a collaborative effort},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {129--142},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0072-z},
doi = {10.1007/S10822-017-0072-Z},
timestamp = {Sat, 30 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GaoHCWAFFWWSVP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GaoLCZH18,
author = {Jian Gao and
Li Liang and
Qingqing Chen and
Ling Zhang and
Tonghui Huang},
title = {Insight into the molecular mechanism of yeast acetyl-coenzyme {A}
carboxylase mutants F510I, N485G, I69E, E477R, and {K73R} resistant
to soraphen {A}},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {4},
pages = {547--557},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0108-z},
doi = {10.1007/S10822-018-0108-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GaoLCZH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GarciaG18,
author = {Gonzalo Cerruela Garc{\'{\i}}a and
Nicol{\'{a}}s Garc{\'{\i}}a{-}Pedrajas},
title = {Boosted feature selectors: a case study on prediction P-gp inhibitors
and substrates},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {11},
pages = {1273--1294},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0171-5},
doi = {10.1007/S10822-018-0171-5},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GarciaG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GasteigerMNOS18,
author = {Johann Gasteiger and
Yvonne C. Martin and
Anthony Nicholls and
Tudor I. Oprea and
Terry R. Stouch},
title = {Leaving us with fond memories, smiles, {SMILES} and, alas, tears:
a tribute to David Weininger, 1952-2016},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {2},
pages = {313--319},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0104-3},
doi = {10.1007/S10822-018-0104-3},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GasteigerMNOS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GhoshJG18,
author = {Shibaji Ghosh and
Kalyanashis Jana and
Bishwajit Ganguly},
title = {Influence of gauche effect on uncharged oxime reactivators for the
reactivation of tabun-inhibited AChE: quantum chemical and steered
molecular dynamics studies},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {7},
pages = {793--807},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0130-1},
doi = {10.1007/S10822-018-0130-1},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GhoshJG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GimadievMNBAV18,
author = {Timur Gimadiev and
Timur I. Madzhidov and
Ramil I. Nugmanov and
Igor I. Baskin and
Igor S. Antipin and
Alexandre Varnek},
title = {Assessment of tautomer distribution using the condensed reaction graph
approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {3},
pages = {401--414},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0101-6},
doi = {10.1007/S10822-018-0101-6},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GimadievMNBAV18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GomesSBR18,
author = {Priscila da Silva Figueiredo Celestino Gomes and
Franck Da Silva and
Guillaume Bret and
Didier Rognan},
title = {Ranking docking poses by graph matching of protein-ligand interactions:
lessons learned from the {D3R} Grand Challenge 2},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {75--87},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0046-1},
doi = {10.1007/S10822-017-0046-1},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GomesSBR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Habgood18,
author = {Matthew Habgood},
title = {Conformational ensemble comparison for small molecules in drug discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {8},
pages = {841--852},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0132-z},
doi = {10.1007/S10822-018-0132-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Habgood18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Hamed18,
author = {Mazen Y. Hamed},
title = {Role of protein structure and the role of individual fingers in zinc
finger protein-DNA recognition: a molecular dynamics simulation study
and free energy calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {6},
pages = {657--669},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0119-9},
doi = {10.1007/S10822-018-0119-9},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Hamed18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HanHJNTB18,
author = {Kyungreem Han and
Phillip S. Hudson and
Michael R. Jones and
Naohiro Nishikawa and
Florentina Tofoleanu and
Bernard R. Brooks},
title = {Prediction of {CB[8]} host-guest binding free energies in {SAMPL6}
using the double-decoupling method},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1059--1073},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0144-8},
doi = {10.1007/S10822-018-0144-8},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HanHJNTB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HasanloeiSSSS18,
author = {Mohammad Amin Valizade Hasanloei and
Razieh Sheikhpour and
Mehdi Agha Sarram and
Elnaz Sheikhpour and
Hamdollah Sharifi},
title = {A combined Fisher and Laplacian score for feature selection in {QSAR}
based drug design using compounds with known and unknown activities},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {2},
pages = {375--384},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0094-6},
doi = {10.1007/S10822-017-0094-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HasanloeiSSSS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HoguesSGCP18,
author = {Herv{\'{e}} Hogues and
Traian Sulea and
Francis Gaudreault and
Christopher R. Corbeil and
Enrico O. Purisima},
title = {Binding pose and affinity prediction in the 2016 {D3R} Grand Challenge
2 using the Wilma-SIE method},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {143--150},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0071-0},
doi = {10.1007/S10822-017-0071-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HoguesSGCP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HuQLPG18,
author = {Wen Hu and
Liu Qin and
Menglong Li and
Xuemei Pu and
Yanzhi Guo},
title = {Individually double minimum-distance definition of protein-RNA binding
residues and application to structure-based prediction},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {12},
pages = {1363--1373},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0177-z},
doi = {10.1007/S10822-018-0177-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HuQLPG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HudsonHWB18,
author = {Phillip S. Hudson and
Kyungreem Han and
H. Lee Woodcock III and
Bernard R. Brooks},
title = {Force matching as a stepping stone to {QM/MM} {CB[8]} host/guest binding
free energies: a {SAMPL6} cautionary tale},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {983--999},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0165-3},
doi = {10.1007/S10822-018-0165-3},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HudsonHWB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HuntST18,
author = {Peter A. Hunt and
Matthew D. Segall and
Jonathan D. Tyzack},
title = {WhichP450: a multi-class categorical model to predict the major metabolising
{CYP450} isoform for a compound},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {4},
pages = {537--546},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0107-0},
doi = {10.1007/S10822-018-0107-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HuntST18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/IsikLRNWWRMMMRC18,
author = {Mehtap Isik and
Dorothy Levorse and
Ari{\"{e}}n S. Rustenburg and
Ikenna E. Ndukwe and
Heather Wang and
Xiao Wang and
Mikhail Y. Reibarkh and
Gary E. Martin and
Alexey A. Makarov and
David L. Mobley and
Timothy Rhodes and
John D. Chodera},
title = {pK a measurements for the {SAMPL6} prediction challenge for a set
of kinase inhibitor-like fragments},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1117--1138},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0168-0},
doi = {10.1007/S10822-018-0168-0},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/IsikLRNWWRMMMRC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JainKE18,
author = {Sankalp Jain and
Eleni Kotsampasakou and
Gerhard F. Ecker},
title = {Comparing the performance of meta-classifiers - a case study on selected
imbalanced data sets relevant for prediction of liver toxicity},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {5},
pages = {583--590},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0116-z},
doi = {10.1007/S10822-018-0116-Z},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JainKE18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KadukovaG18,
author = {Maria Kadukova and
Sergei Grudinin},
title = {Docking of small molecules to farnesoid {X} receptors using AutoDock
Vina with the Convex-PL potential: lessons learned from {D3R} Grand
Challenge 2},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {151--162},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0062-1},
doi = {10.1007/S10822-017-0062-1},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KadukovaG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KumarZ18,
author = {Ashutosh Kumar and
Kam Y. J. Zhang},
title = {A cross docking pipeline for improving pose prediction and virtual
screening performance},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {163--173},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0048-z},
doi = {10.1007/S10822-017-0048-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KumarZ18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KunimotoB18,
author = {Ryo Kunimoto and
J{\"{u}}rgen Bajorath},
title = {Design of a tripartite network for the prediction of drug targets},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {2},
pages = {321--330},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0098-x},
doi = {10.1007/S10822-018-0098-X},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KunimotoB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KurkcuogluKCTRM18,
author = {Zeynep Kurkcuoglu and
Panagiotis I. Koukos and
Nevia Citro and
Mikael E. Trellet and
Jo{\~{a}}o P. G. L. M. Rodrigues and
Irina S. Moreira and
Jorge Roel{-}Touris and
Adrien S. J. Melquiond and
Cunliang Geng and
J{\"{o}}rg Schaarschmidt and
Li C. Xue and
Anna Vangone and
Alexandre M. J. J. Bonvin},
title = {Performance of {HADDOCK} and a simple contact-based protein-ligand
binding affinity predictor in the {D3R} Grand Challenge 2},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {175--185},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0049-y},
doi = {10.1007/S10822-017-0049-Y},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KurkcuogluKCTRM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LamAT18,
author = {Polo Chun{-}Hung Lam and
Ruben Abagyan and
Maxim Totrov},
title = {Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor
structure-based approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {187--198},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0058-x},
doi = {10.1007/S10822-017-0058-X},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LamAT18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LauryWGP18,
author = {Marie L. Laury and
Zhi Wang and
Aaron S. Gordon and
Jay W. Ponder},
title = {Absolute binding free energies for the {SAMPL6} cucurbit[8]uril host-guest
challenge via the {AMOEBA} polarizable force field},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1087--1095},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0147-5},
doi = {10.1007/S10822-018-0147-5},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LauryWGP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LehertePJVL18,
author = {Laurence Leherte and
Axel Petit and
Denis Jacquemin and
Daniel P. Vercauteren and
Ad{\`{e}}le D. Laurent},
title = {Investigating cyclic peptides inhibiting {CD2-CD58} interactions through
molecular dynamics and molecular docking methods},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {11},
pages = {1295--1313},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0172-4},
doi = {10.1007/S10822-018-0172-4},
timestamp = {Tue, 16 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LehertePJVL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LenzW18,
author = {Stefan A. P. Lenz and
Stacey D. Wetmore},
title = {Structural explanation for the tunable substrate specificity of an
E. coli nucleoside hydrolase: insights from molecular dynamics simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {12},
pages = {1375--1388},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0178-y},
doi = {10.1007/S10822-018-0178-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LenzW18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiPLZLLZ18,
author = {Yaping Li and
Yinglan Pu and
Hui Liu and
Li Zhang and
Xingyong Liu and
Yan Li and
Zhili Zuo},
title = {Discovery of novel wee1 inhibitors via structure-based virtual screening
and biological evaluation},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {9},
pages = {901--915},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0122-1},
doi = {10.1007/S10822-018-0122-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiPLZLLZ18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LuY18,
author = {Lu Lu and
Hua Yu},
title = {{DR2DI:} a powerful computational tool for predicting novel drug-disease
associations},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {5},
pages = {633--642},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0117-y},
doi = {10.1007/S10822-018-0117-Y},
timestamp = {Mon, 10 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LuY18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MaCJKYLCN18,
author = {Songling Ma and
Jiwon Choi and
Xuemei Jin and
Hyun{-}Yi Kim and
Jihye Yun and
Weontae Lee and
Kang{-}Yell Choi and
Kyoung Tai No},
title = {Discovery of a small-molecule inhibitor of Dvl-CXXC5 interaction by
computational approaches},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {5},
pages = {643--655},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0118-x},
doi = {10.1007/S10822-018-0118-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MaCJKYLCN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Majerz18,
author = {Irena Majerz},
title = {Weak interactions in furan dimers},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {11},
pages = {1247--1258},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0163-5},
doi = {10.1007/S10822-018-0163-5},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Majerz18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ManzoniR18,
author = {Francesco Manzoni and
Ulf Ryde},
title = {Assessing the stability of free-energy perturbation calculations by
performing variations in the method},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {4},
pages = {529--536},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0110-5},
doi = {10.1007/S10822-018-0110-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ManzoniR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MargiottaDM18,
author = {Enrico Margiotta and
Giuseppe Deganutti and
Stefano Moro},
title = {Could the presence of sodium ion influence the accuracy and precision
of the ligand-posing in the human {A2A} adenosine receptor orthosteric
binding site using a molecular docking approach? Insights from Dockbench},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {12},
pages = {1337--1346},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0174-2},
doi = {10.1007/S10822-018-0174-2},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MargiottaDM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Martin18,
author = {Yvonne C. Martin},
title = {How medicinal chemists learned about log {P}},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {8},
pages = {809--819},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0127-9},
doi = {10.1007/S10822-018-0127-9},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Martin18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MartinsTOPCF18,
author = {Luan Carvalho Martins and
Pedro Henrique Monteiro Torres and
Renata Barbosa de Oliveira and
Pedro Geraldo Pascutti and
Elio A. Cino and
Rafaela Salgado Ferreira},
title = {Investigation of the binding mode of a novel cruzain inhibitor by
docking, molecular dynamics, ab initio and {MM/PBSA} calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {5},
pages = {591--605},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0112-3},
doi = {10.1007/S10822-018-0112-3},
timestamp = {Thu, 11 Mar 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/MartinsTOPCF18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MeyJM18,
author = {Antonia S. J. S. Mey and
Jordi Ju{\'{a}}rez Jim{\'{e}}nez and
Julien Michel},
title = {Impact of domain knowledge on blinded predictions of binding energies
by alchemical free energy calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {199--210},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0083-9},
doi = {10.1007/S10822-017-0083-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MeyJM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MiyaoB18,
author = {Tomoyuki Miyao and
J{\"{u}}rgen Bajorath},
title = {Exploring ensembles of bioactive or virtual analogs of X-ray ligands
for shape similarity searching},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {7},
pages = {759--767},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0128-8},
doi = {10.1007/S10822-018-0128-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MiyaoB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NagarajanV18,
author = {Hemavathy Nagarajan and
Umashankar Vetrivel},
title = {Demystifying the pH dependent conformational changes of human heparanase
pertaining to structure-function relationships: an in silico approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {8},
pages = {821--840},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0131-0},
doi = {10.1007/S10822-018-0131-0},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NagarajanV18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NascimentoOA18,
author = {{\'{E}}rica C. M. Nascimento and
M{\'{o}}nica Oliva and
Juan Andr{\'{e}}s},
title = {Binding free energy calculations to rationalize the interactions of
huprines with acetylcholinesterase},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {5},
pages = {607--622},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0114-1},
doi = {10.1007/S10822-018-0114-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NascimentoOA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NguyenJR18,
author = {Minh Khoa Nguyen and
L{\'{e}}onard Jaillet and
St{\'{e}}phane Redon},
title = {Generating conformational transition paths with low potential-energy
barriers for proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {8},
pages = {853--867},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0137-7},
doi = {10.1007/S10822-018-0137-7},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NguyenJR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NikitinaIT18,
author = {Natalia Nikitina and
Evgeny Ivashko and
Andrei Tchernykh},
title = {Congestion game scheduling for virtual drug screening optimization},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {2},
pages = {363--374},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0093-7},
doi = {10.1007/S10822-017-0093-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NikitinaIT18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NishikawaHWTB18,
author = {Naohiro Nishikawa and
Kyungreem Han and
Xiongwu Wu and
Florentina Tofoleanu and
Bernard R. Brooks},
title = {Comparison of the umbrella sampling and the double decoupling method
in binding free energy predictions for {SAMPL6} octa-acid host-guest
challenges},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1075--1086},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0166-2},
doi = {10.1007/S10822-018-0166-2},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NishikawaHWTB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NtombelaFIGMLKH18,
author = {Thandokuhle Ntombela and
Zeynab Fakhar and
Collins U. Ibeji and
Thavendran Govender and
Glenn E. M. Maguire and
Gyanu Lamichhane and
Hendrik G. Kruger and
Bahareh Honarparvar},
title = {Molecular insight on the non-covalent interactions between carbapenems
and l, d-transpeptidase 2 from Mycobacterium tuberculosis: {ONIOM}
study},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {6},
pages = {687--701},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0121-2},
doi = {10.1007/S10822-018-0121-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NtombelaFIGMLKH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OlssonGR18,
author = {Martin A. Olsson and
Alfonso T. Garc{\'{\i}}a{-}Sosa and
Ulf Ryde},
title = {Binding affinities of the farnesoid {X} receptor in the {D3R} Grand
Challenge 2 estimated by free-energy perturbation and docking},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {211--224},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0056-z},
doi = {10.1007/S10822-017-0056-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OlssonGR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OrgovanFSSBK18,
author = {Zolt{\'{a}}n Orgov{\'{a}}n and
Gy{\"{o}}rgy G. Ferenczy and
Thomas Steinbrecher and
Bence Szil{\'{a}}gyi and
D{\'{a}}vid Bajusz and
Gy{\"{o}}rgy M. Keser{\"{u}}},
title = {Validation of tautomeric and protomeric binding modes by free energy
calculations. {A} case study for the structure based optimization
of d-amino acid oxidase inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {2},
pages = {331--345},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0097-y},
doi = {10.1007/S10822-018-0097-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OrgovanFSSBK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PadhornyHMMMABK18,
author = {Dzmitry Padhorny and
David R. Hall and
Hanieh Mirzaei and
Artem B. Mamonov and
Mohammad Moghadasi and
Andrey Alekseenko and
Dmitri Beglov and
Dima Kozakov},
title = {Protein-ligand docking using {FFT} based sampling: {D3R} case study},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {225--230},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0069-7},
doi = {10.1007/S10822-017-0069-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PadhornyHMMMABK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PapadourakisBM18,
author = {Michail Papadourakis and
Stefano Bosisio and
Julien Michel},
title = {Blinded predictions of standard binding free energies: lessons learned
from the {SAMPL6} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1047--1058},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0154-6},
doi = {10.1007/S10822-018-0154-6},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PapadourakisBM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PatraGBC18,
author = {Piya Patra and
Mahua Ghosh and
Raja Banerjee and
Jaydeb Chakrabarti},
title = {Quantum chemical studies on anion specificity of C{\(\alpha\)}NN motif
in functional proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {9},
pages = {929--936},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0157-3},
doi = {10.1007/S10822-018-0157-3},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PatraGBC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PaulG18,
author = {D. Sam Paul and
N. Gautham},
title = {Protein-small molecule docking with receptor flexibility in iMOLSDOCK},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {9},
pages = {889--900},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0152-8},
doi = {10.1007/S10822-018-0152-8},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PaulG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PrachtWURG18,
author = {Philipp Pracht and
Rainer Wilcken and
Anik{\'{o}} Udvarhelyi and
Stephane Rodde and
Stefan Grimme},
title = {High accuracy quantum-chemistry-based calculation and blind prediction
of macroscopic pKa values in the context of the {SAMPL6} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1139--1149},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0145-7},
doi = {10.1007/S10822-018-0145-7},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PrachtWURG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PrasadHZB18,
author = {Samarjeet Prasad and
Jing Huang and
Qiao Zeng and
Bernard R. Brooks},
title = {An explicit-solvent hybrid {QM} and {MM} approach for predicting pKa
of small molecules in {SAMPL6} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1191--1201},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0167-1},
doi = {10.1007/S10822-018-0167-1},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/PrasadHZB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ProcacciGG18,
author = {Piero Procacci and
Massimiliano Guarrasi and
Guido Guarnieri},
title = {{SAMPL6} host-guest blind predictions using a non equilibrium alchemical
approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {965--982},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0151-9},
doi = {10.1007/S10822-018-0151-9},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ProcacciGG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RaschkaSLGHLK18,
author = {Sebastian Raschka and
Anne M. Scott and
Nan Liu and
Santosh Gunturu and
Mar Huertas and
Weiming Li and
Leslie A. Kuhn},
title = {Enabling the hypothesis-driven prioritization of ligand candidates
in big databases: Screenlamp and its application to {GPCR} inhibitor
discovery for invasive species control},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {3},
pages = {415--433},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0100-7},
doi = {10.1007/S10822-018-0100-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RaschkaSLGHLK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RaschkaWBK18,
author = {Sebastian Raschka and
Alex J. Wolf and
Joseph Bemister{-}Buffington and
Leslie A. Kuhn},
title = {Protein-ligand interfaces are polarized: discovery of a strong trend
for intermolecular hydrogen bonds to favor donors on the protein side
with implications for predicting and designing ligand complexes},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {4},
pages = {511--528},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0105-2},
doi = {10.1007/S10822-018-0105-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RaschkaWBK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RatameroBDR18,
author = {Erick Martins Ratamero and
Dom Bellini and
Christopher G. Dowson and
Rudolf A. R{\"{o}}mer},
title = {Touching proteins with virtual bare hands - Visualizing protein-drug
complexes and their dynamics in self-made virtual reality using gaming
hardware},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {6},
pages = {703--709},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0123-0},
doi = {10.1007/S10822-018-0123-0},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RatameroBDR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ReauLZM18,
author = {Manon R{\'{e}}au and
Florent Langenfeld and
Jean{-}Fran{\c{c}}ois Zagury and
Matthieu Mont{\`{e}}s},
title = {Predicting the affinity of Farnesoid {X} Receptor ligands through
a hierarchical ranking protocol: a {D3R} Grand Challenge 2 case study},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {231--238},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0063-0},
doi = {10.1007/S10822-017-0063-0},
timestamp = {Thu, 12 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ReauLZM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RifaiDVG18,
author = {Eko Aditya Rifai and
Marc van Dijk and
Nico P. E. Vermeulen and
Daan P. Geerke},
title = {Binding free energy predictions of farnesoid {X} receptor {(FXR)}
agonists using a linear interaction energy {(LIE)} approach with reliability
estimation: application to the {D3R} Grand Challenge 2},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {239--249},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0055-0},
doi = {10.1007/S10822-017-0055-0},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/RifaiDVG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RizziMMYSGCIGMC18,
author = {Andrea Rizzi and
Steven Murkli and
John N. McNeill and
Wei Yao and
Matthew R. Sullivan and
Michael K. Gilson and
Michael Chiu and
Lyle Isaacs and
Bruce C. Gibb and
David L. Mobley and
John D. Chodera},
title = {Overview of the {SAMPL6} host-guest binding affinity prediction challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {937--963},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0170-6},
doi = {10.1007/S10822-018-0170-6},
timestamp = {Fri, 18 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/RizziMMYSGCIGMC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SabatinoRPFTAAM18,
author = {Manuela Sabatino and
Dante Rotili and
Alexandros Patsilinakos and
Mariantonietta Forgione and
Daniela Tomaselli and
Fr{\'{e}}deric Alby and
Paola B. Arimondo and
Antonello Mai and
Rino Ragno},
title = {Disruptor of telomeric silencing 1-like {(DOT1L):} disclosing a new
class of non-nucleoside inhibitors by means of ligand-based and structure-based
approaches},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {3},
pages = {435--458},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0096-z},
doi = {10.1007/S10822-018-0096-Z},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SabatinoRPFTAAM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SalmasoSCM18,
author = {Veronica Salmaso and
Mattia Sturlese and
Alberto Cuzzolin and
Stefano Moro},
title = {Combining self- and cross-docking as benchmark tools: the performance
of DockBench in the {D3R} Grand Challenge 2},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {251--264},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0051-4},
doi = {10.1007/S10822-017-0051-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SalmasoSCM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SanusiGMMLKH18,
author = {Zainab K. Sanusi and
Thavendran Govender and
Glenn E. M. Maguire and
Sibusiso B. Maseko and
Johnson Lin and
Hendrik G. Kruger and
Bahareh Honarparvar},
title = {An insight to the molecular interactions of the {FDA} approved {HIV}
{PR} drugs against L38L{\(\uparrow\)}N{\(\uparrow\)}L {PR} mutant},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {3},
pages = {459--471},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0099-9},
doi = {10.1007/S10822-018-0099-9},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SanusiGMMLKH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SchindlerRK18,
author = {Christina E. M. Schindler and
Friedrich Rippmann and
Daniel Kuhn},
title = {Relative binding affinity prediction of farnesoid {X} receptor in
the {D3R} Grand Challenge 2 using {FEP+}},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {265--272},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0064-z},
doi = {10.1007/S10822-017-0064-Z},
timestamp = {Thu, 07 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SchindlerRK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SelwaEZI18,
author = {Edithe Selwa and
Eddy Elis{\'{e}}e and
Agustin Zavala and
Bogdan I. Iorga},
title = {Blinded evaluation of farnesoid {X} receptor {(FXR)} ligands binding
using molecular docking and free energy calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {273--286},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0054-1},
doi = {10.1007/S10822-017-0054-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SelwaEZI18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SelwaKBI18,
author = {Edithe Selwa and
Ian M. Kenney and
Oliver Beckstein and
Bogdan I. Iorga},
title = {{SAMPL6:} calculation of macroscopic pK a values from ab initio quantum
mechanical free energies},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1203--1216},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0138-6},
doi = {10.1007/S10822-018-0138-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SelwaKBI18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SianiKOD18,
author = {Paulo Siani and
Himanshu Khandelia and
M. Orsi and
Luis Gustavo Dias},
title = {Parameterization of a coarse-grained model of cholesterol with point-dipole
electrostatics},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {11},
pages = {1259--1271},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0164-4},
doi = {10.1007/S10822-018-0164-4},
timestamp = {Mon, 04 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SianiKOD18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SinghBWRG18,
author = {Krishna P. Singh and
Lokesh Baweja and
Olaf Wolkenhauer and
Qamar Rahman and
Shailendra K. Gupta},
title = {Impact of graphene-based nanomaterials (GBNMs) on the structural and
functional conformations of hepcidin peptide},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {3},
pages = {487--496},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0103-4},
doi = {10.1007/S10822-018-0103-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SinghBWRG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SongBZM18,
author = {Lin Frank Song and
Nupur Bansal and
Zheng Zheng and
Kenneth M. Merz Jr.},
title = {Detailed potential of mean force studies on host-guest systems from
the {SAMPL6} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1013--1026},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0153-7},
doi = {10.1007/S10822-018-0153-7},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SongBZM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SrinivasanR18,
author = {E. Srinivasan and
R. Rajasekaran},
title = {Quantum chemical and molecular mechanics studies on the assessment
of interactions between resveratrol and mutant {SOD1} {(G93A)} protein},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {12},
pages = {1347--1361},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0175-1},
doi = {10.1007/S10822-018-0175-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SrinivasanR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TielkerEGK18,
author = {Nicolas Tielker and
Lukas Eberlein and
Stefan G{\"{u}}ssregen and
Stefan M. Kast},
title = {The {SAMPL6} challenge on predicting aqueous pK a values from {EC-RISM}
theory},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1151--1163},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0140-z},
doi = {10.1007/S10822-018-0140-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TielkerEGK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TripathiSSPNS18,
author = {Shubhandra Tripathi and
Gaurava Srivastava and
Aastha Singh and
A. P. Prakasham and
Arvind S. Negi and
Ashok Sharma},
title = {Insight into microtubule destabilization mechanism of 3, 4, 5-trimethoxyphenyl
indanone derivatives using molecular dynamics simulation and conformational
modes analysis},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {4},
pages = {559--572},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0109-y},
doi = {10.1007/S10822-018-0109-Y},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/TripathiSSPNS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TshepelevitshHL18,
author = {Sofja Tshepelevitsh and
Kertu Hernits and
Ivo Leito},
title = {Prediction of partition and distribution coefficients in various solvent
pairs with {COSMO-RS}},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {6},
pages = {711--722},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0125-y},
doi = {10.1007/S10822-018-0125-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TshepelevitshHL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VettorazziMGAAE18,
author = {Marcela Vettorazzi and
Cintia Men{\'{e}}ndez and
Lucas Gutierrez and
Sebastian A. Andujar and
Gustavo Appignanesi and
Ricardo D. Enriz},
title = {Theoretical models to predict the inhibitory effect of ligands of
sphingosine kinase 1 using {QTAIM} calculations and hydrogen bond
dynamic propensity analysis},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {7},
pages = {781--791},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0129-7},
doi = {10.1007/S10822-018-0129-7},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/VettorazziMGAAE18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VillaLCGLBIMBG18,
author = {Stefania Villa and
Laura Legnani and
Diego Colombo and
Arianna Gelain and
Carmen Lammi and
Daniele Bongiorno and
Denise P. Ilboudo and
Kellen E. McGee and
J{\"{u}}rgen Bosch and
Giovanni Grazioso},
title = {Structure-based drug design, synthesis and biological assays of P.
falciparum Atg3-Atg8 protein-protein interaction inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {3},
pages = {473--486},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0102-5},
doi = {10.1007/S10822-018-0102-5},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/VillaLCGLBIMBG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WingertOC18,
author = {Bentley M. Wingert and
Rick Oerlemans and
Carlos J. Camacho},
title = {Optimal affinity ranking for automated virtual screening validated
in prospective {D3R} grand challenges},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {287--297},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0065-y},
doi = {10.1007/S10822-017-0065-Y},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WingertOC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Winkler18,
author = {David A. Winkler},
title = {Sparse {QSAR} modelling methods for therapeutic and regenerative medicine},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {4},
pages = {497--509},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0106-1},
doi = {10.1007/S10822-018-0106-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Winkler18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/XueZSZHJS18,
author = {Youlin Xue and
Qiaoshi Zhang and
Yuna Sun and
Xiaohong Zhou and
Ian P. Hurley and
Gary W. Jones and
Youtao Song},
title = {Using steered molecular dynamics to study the interaction between
{ADP} and the nucleotide-binding domain of yeast Hsp70 protein Ssa1},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {11},
pages = {1217--1227},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0136-8},
doi = {10.1007/S10822-018-0136-8},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/XueZSZHJS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YakovenkoJ18,
author = {Oleksandr Yakovenko and
Steven J. M. Jones},
title = {Modern drug design: the implication of using artificial neuronal networks
and multiple molecular dynamic simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {299--311},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0085-7},
doi = {10.1007/S10822-017-0085-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YakovenkoJ18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YamaotsuH18,
author = {Noriyuki Yamaotsu and
Shuichi Hirono},
title = {In silico fragment-mapping method: a new tool for fragment-based/structure-based
drug discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {11},
pages = {1229--1245},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0160-8},
doi = {10.1007/S10822-018-0160-8},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YamaotsuH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YuGX18,
author = {Miao Yu and
Qiong Gu and
Jun Xu},
title = {Discovering new PI3K{\(\alpha\)} inhibitors with a strategy of combining
ligand-based and structure-based virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {2},
pages = {347--361},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0092-8},
doi = {10.1007/S10822-017-0092-8},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/YuGX18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZengJB18,
author = {Qiao Zeng and
Michael R. Jones and
Bernard R. Brooks},
title = {Absolute and relative pK a predictions via a {DFT} approach applied
to the {SAMPL6} blind challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {10},
pages = {1179--1189},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0150-x},
doi = {10.1007/S10822-018-0150-X},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZengJB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhangCRHHHWSZCL18,
author = {Xin Zhang and
Jason B. Cross and
Jan Romero and
Alexander Heifetz and
Eric Humphries and
Katie Hall and
Yuchuan Wu and
Sabrina Stucka and
Jing Zhang and
Haoqun Chandonnet and
Blaise Lippa and
M. Dominic Ryan and
J. Christian Baber},
title = {In-silico guided discovery of novel {CCR9} antagonists},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {4},
pages = {573--582},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0113-2},
doi = {10.1007/S10822-018-0113-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZhangCRHHHWSZCL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZheninBMVSH18,
author = {Michael Zhenin and
Malkeet Singh Bahia and
Gilles Marcou and
Alexandre Varnek and
Hanoch Senderowitz and
Dragos Horvath},
title = {Rescoring of docking poses under Occam's Razor: are there simpler
solutions?},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {9},
pages = {877--888},
year = {2018},
url = {https://doi.org/10.1007/s10822-018-0155-5},
doi = {10.1007/S10822-018-0155-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZheninBMVSH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AkamatsuO17,
author = {Miki Akamatsu and
Tudor I. Oprea},
title = {Obituary: Toshio Fujita, {QSAR} pioneer},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {959--960},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0078-6},
doi = {10.1007/S10822-017-0078-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AkamatsuO17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Al-DabbaghSHAS17,
author = {Mohammed Mumtaz Al{-}Dabbagh and
Naomie Salim and
Mubarak Himmat and
Ali Ahmed and
Faisal Saeed},
title = {Quantum probability ranking principle for ligand-based virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {365--378},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0003-4},
doi = {10.1007/S10822-016-0003-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Al-DabbaghSHAS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AlbaMPMMD17,
author = {Josephine Alba and
Maria Jose Marcaida and
Jes{\'{u}}s Prieto and
Guillermo Montoya and
Rafael Molina and
Marco D'Abramo},
title = {Structure and dynamics of mesophilic variants from the homing endonuclease
I-DmoI},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {12},
pages = {1063--1072},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0087-5},
doi = {10.1007/S10822-017-0087-5},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AlbaMPMMD17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Badalkhani-Khamseh17,
author = {Farideh Badalkhani{-}Khamseh and
Azadeh Ebrahim{-}Habibi and
Nasser L. Hadipour},
title = {Atomistic computer simulations on multi-loaded {PAMAM} dendrimers:
a comparison of amine- and hydroxyl-terminated dendrimers},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {12},
pages = {1097--1111},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0091-9},
doi = {10.1007/S10822-017-0091-9},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Badalkhani-Khamseh17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BaekSCS17,
author = {Minkyung Baek and
Woong{-}Hee Shin and
Hwan Won Chung and
Chaok Seok},
title = {GalaxyDock {BP2} score: a hybrid scoring function for accurate protein-ligand
docking},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {653--666},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0030-9},
doi = {10.1007/S10822-017-0030-9},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BaekSCS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BansalZCM17,
author = {Nupur Bansal and
Zheng Zheng and
David S. Cerutti and
Kenneth M. Merz Jr.},
title = {On the fly estimation of host-guest binding free energies using the
movable type method: participation in the {SAMPL5} blind challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {47--60},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9980-6},
doi = {10.1007/S10822-016-9980-6},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BansalZCM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BaskinSBV17,
author = {Igor I. Baskin and
Vitaly P. Solov'ev and
Alexander A. Bagatur'yants and
Alexandre Varnek},
title = {Predictive cartography of metal binders using generative topographic
mapping},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {701--714},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0033-6},
doi = {10.1007/S10822-017-0033-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BaskinSBV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BasuSW17,
author = {Sankar Basu and
Fredrik S{\"{o}}derquist and
Bj{\"{o}}rn Wallner},
title = {Proteus: a random forest classifier to predict disorder-to-order transitioning
binding regions in intrinsically disordered proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {5},
pages = {453--466},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0020-y},
doi = {10.1007/S10822-017-0020-Y},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/BasuSW17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BehrenR17,
author = {Mathias M. von Behren and
Matthias Rarey},
title = {Ligand-based virtual screening under partial shape constraints},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {335--347},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0011-z},
doi = {10.1007/S10822-017-0011-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BehrenR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BhakatS17,
author = {Soumendranath Bhakat and
P{\"{a}}r S{\"{o}}derhjelm},
title = {Resolving the problem of trapped water in binding cavities: prediction
of host-guest binding free energies in the {SAMPL5} challenge by funnel
metadynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {119--132},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9948-6},
doi = {10.1007/S10822-016-9948-6},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BhakatS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BhattacharyyaHB17,
author = {Dhananjay Bhattacharyya and
Sukanya Halder and
Sankar Basu and
Debasish Mukherjee and
Prasun Kumar and
Manju Bansal},
title = {RNAHelix: computational modeling of nucleic acid structures with Watson-Crick
and non-canonical base pairs},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {2},
pages = {219--235},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0007-0},
doi = {10.1007/S10822-016-0007-0},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/BhattacharyyaHB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BorgesKMPRRS17,
author = {N{\'{a}}dia Melo Borges and
Peter W. Kenny and
Carlos A. Montanari and
Igor M. Prokopczyk and
Jean F. R. Ribeiro and
Josmar R. Rocha and
Geraldo Rodrigues Sartori},
title = {The influence of hydrogen bonding on partition coefficients},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {2},
pages = {163--181},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0002-5},
doi = {10.1007/S10822-016-0002-5},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BorgesKMPRRS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BosisioMM17,
author = {Stefano Bosisio and
Antonia S. J. S. Mey and
Julien Michel},
title = {Blinded predictions of host-guest standard free energies of binding
in the {SAMPL5} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {61--70},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9933-0},
doi = {10.1007/S10822-016-9933-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BosisioMM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BrownSJHS17,
author = {Frank K. Brown and
Edward C. Sherer and
Scott A. Johnson and
M. Katharine Holloway and
Bradley Sherborne},
title = {The evolution of drug design at Merck Research Laboratories},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {255--266},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9993-1},
doi = {10.1007/S10822-016-9993-1},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/BrownSJHS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CaiLLDYGX17,
author = {Jie Cai and
Chanjuan Li and
Zhihong Liu and
Jiewen Du and
Jiming Ye and
Qiong Gu and
Jun Xu},
title = {Predicting {DPP-IV} inhibitors with machine learning approaches},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {393--402},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0009-6},
doi = {10.1007/S10822-017-0009-6},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CaiLLDYGX17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CaldararuORNR17,
author = {Octav Caldararu and
Martin A. Olsson and
Christoph Riplinger and
Frank Neese and
Ulf Ryde},
title = {Binding free energies in the {SAMPL5} octa-acid host-guest challenge
calculated with {DFT-D3} and {CCSD(T)}},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {87--106},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9957-5},
doi = {10.1007/S10822-016-9957-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CaldararuORNR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CaoNJTS17,
author = {Han Cao and
Marcus C. K. Ng and
Siti Azma Jusoh and
Hio Kuan Tai and
Shirley W. I. Siu},
title = {{TMDIM:} an improved algorithm for the structure prediction of transmembrane
domains of bitopic dimers},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {855--865},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0047-0},
doi = {10.1007/S10822-017-0047-0},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CaoNJTS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CardamoneICFD17,
author = {Francesca Cardamone and
Federico Iacovelli and
Giovanni Chillemi and
Mattia Falconi and
Alessandro Desideri},
title = {A molecular dynamics simulation study decodes the early stage of the
disassembly process abolishing the human {SAMHD1} function},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {5},
pages = {497--505},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0014-9},
doi = {10.1007/S10822-017-0014-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CardamoneICFD17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Chan17,
author = {Shek Ling Chan},
title = {MolAlign: an algorithm for aligning multiple small molecules},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {6},
pages = {523--546},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0023-8},
doi = {10.1007/S10822-017-0023-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Chan17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CifciAAM17,
author = {G{\"{u}}lsah {\c{C}}ifci and
Viktorya Aviyente and
E. Demet Akten and
Gerald Monard},
title = {Assessing protein-ligand binding modes with computational tools: the
case of {PDE4B}},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {6},
pages = {563--575},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0024-7},
doi = {10.1007/S10822-017-0024-7},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CifciAAM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ClevesJ17,
author = {Ann E. Cleves and
Ajay N. Jain},
title = {ForceGen 3D structure and conformer generation: from small lead-like
molecules to macrocyclic drugs},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {5},
pages = {419--439},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0015-8},
doi = {10.1007/S10822-017-0015-8},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ClevesJ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CoxPSNLOBRP17,
author = {Courtney E. Cox and
Jeremy R. Phifer and
Larissa Ferreira da Silva and
Gabriel Gon{\c{c}}alves Nogueira and
Ryan T. Ley and
Elizabeth J. O'Loughlin and
Ana Karolyne Pereira Barbosa and
Brett T. Rygelski and
Andrew S. Paluch},
title = {Combining {MOSCED} with molecular simulation free energy calculations
or electronic structure calculations to develop an efficient tool
for solvent formulation and selection},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {2},
pages = {183--199},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0001-6},
doi = {10.1007/S10822-016-0001-6},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/CoxPSNLOBRP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DahanMKKAZB17,
author = {Arik Dahan and
Milica Markovic and
Shahar Keinan and
Igor Kurnikov and
Aaron Aponick and
Ellen M. Zimmermann and
Shimon Ben{-}Shabat},
title = {Computational modeling and in-vitro/in-silico correlation of phospholipid-based
prodrugs for targeted drug delivery in inflammatory bowel disease},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {1021--1028},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0079-5},
doi = {10.1007/S10822-017-0079-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DahanMKKAZB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DimovaB17,
author = {Dilyana Dimova and
J{\"{u}}rgen Bajorath},
title = {Is scaffold hopping a reliable indicator for the ability of computational
methods to identify structurally diverse active compounds?},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {603--608},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0032-7},
doi = {10.1007/S10822-017-0032-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DimovaB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DuLGYY17,
author = {Juan Du and
Lin Liu and
Li Zhong Guo and
Xiaojun Yao and
Jian Ming Yang},
title = {Molecular basis of {P450} OleTJE: an investigation of substrate binding
mechanism and major pathways},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {5},
pages = {483--495},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0013-x},
doi = {10.1007/S10822-017-0013-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DuLGYY17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FernandezROCVF17,
author = {David Fern{\'{a}}ndez and
Rafael Ramis and
Joaqu{\'{\i}}n Ortega{-}Castro and
Rodrigo Casasnovas and
Bartolom{\'{e}} Vilanova and
Juan Frau},
title = {New insights into human farnesyl pyrophosphate synthase inhibition
by second-generation bisphosphonate drugs},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {675--688},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0034-5},
doi = {10.1007/S10822-017-0034-5},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FernandezROCVF17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GaoWHYZ17,
author = {Qi Gao and
Yijun Wang and
Jiaying Hou and
Qizheng Yao and
Ji Zhang},
title = {Multiple receptor-ligand based pharmacophore modeling and molecular
docking to screen the selective inhibitors of matrix metalloproteinase-9
from natural products},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {625--641},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0028-3},
doi = {10.1007/S10822-017-0028-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GaoWHYZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GeKMLLM17,
author = {Yushu Ge and
Marc van der Kamp and
Maturos Malaisree and
Dan Liu and
Yi Liu and
Adrian J. Mulholland},
title = {Identification of the quinolinedione inhibitor binding site in Cdc25
phosphatase {B} through docking and molecular dynamics simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {995--1007},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0073-y},
doi = {10.1007/S10822-017-0073-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GeKMLLM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Genheden17,
author = {Samuel Genheden},
title = {Solvation free energies and partition coefficients with the coarse-grained
and hybrid all-atom/coarse-grained {MARTINI} models},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {867--876},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0059-9},
doi = {10.1007/S10822-017-0059-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Genheden17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GhanakotaC17,
author = {Phani Ghanakota and
Heather A. Carlson},
title = {Comparing pharmacophore models derived from crystallography and {NMR}
ensembles},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {979--993},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0077-7},
doi = {10.1007/S10822-017-0077-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GhanakotaC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GhoshCJG17,
author = {Shibaji Ghosh and
Nellore Bhanu Chandar and
Kalyanashis Jana and
Bishwajit Ganguly},
title = {Revealing the importance of linkers in K-series oxime reactivators
for tabun-inhibited AChE using quantum chemical, docking and {SMD}
studies},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {729--742},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0036-3},
doi = {10.1007/S10822-017-0036-3},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GhoshCJG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GoldmannZDE17,
author = {Daria Goldmann and
Barbara Zdrazil and
Daniela Digles and
Gerhard F. Ecker},
title = {Empowering pharmacoinformatics by linked life science data},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {319--328},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9990-4},
doi = {10.1007/S10822-016-9990-4},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GoldmannZDE17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Habgood17,
author = {Matthew Habgood},
title = {Bioactive focus in conformational ensembles: a pluralistic approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {12},
pages = {1073--1083},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0089-3},
doi = {10.1007/S10822-017-0089-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Habgood17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/IkebataHIMY17,
author = {Hisaki Ikebata and
Kenta Hongo and
Tetsu Isomura and
Ryo Maezono and
Ryo Yoshida},
title = {Bayesian molecular design with a chemical language model},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {379--391},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0008-z},
doi = {10.1007/S10822-016-0008-Z},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/IkebataHIMY17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/IwaokaSSDSMHOH17,
author = {Michio Iwaoka and
Toshiki Suzuki and
Yuya Shoji and
Kenichi Dedachi and
Taku Shimosato and
Toshiya Minezaki and
Hironobu Hojo and
Hiroyuki Onuki and
Hiroshi Hirota},
title = {Development of {SAAP3D} force field and the application to replica-exchange
Monte Carlo simulation for chignolin and C-peptide},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {12},
pages = {1039--1052},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0084-8},
doi = {10.1007/S10822-017-0084-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/IwaokaSSDSMHOH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JainGRE17,
author = {Sankalp Jain and
Melanie Grandits and
Lars Richter and
Gerhard F. Ecker},
title = {Structure based classification for bile salt export pump {(BSEP)}
inhibitors using comparative structural modeling of human {BSEP}},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {6},
pages = {507--521},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0021-x},
doi = {10.1007/S10822-017-0021-X},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JainGRE17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JedwabnyPDWS17,
author = {Wiktoria Jedwabny and
Joanna Panecka{-}Hofman and
Edyta Dyguda{-}Kazimierowicz and
Rebecca C. Wade and
W. Andrzej Sokalski},
title = {Application of a simple quantum chemical approach to ligand fragment
scoring for Trypanosoma brucei pteridine reductase 1 inhibition},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {715--728},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0035-4},
doi = {10.1007/S10822-017-0035-4},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JedwabnyPDWS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KadukovaG17,
author = {Maria Kadukova and
Sergei Grudinin},
title = {Convex-PL: a novel knowledge-based potential for protein-ligand interactions
deduced from structural databases using convex optimization},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {943--958},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0068-8},
doi = {10.1007/S10822-017-0068-8},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KadukovaG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KayasthaKHVB17,
author = {Shilva Kayastha and
Ryo Kunimoto and
Dragos Horvath and
Alexandre Varnek and
J{\"{u}}rgen Bajorath},
title = {From bird's eye views to molecular communities: two-layered visualization
of structure-activity relationships in large compound data sets},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {961--977},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0070-1},
doi = {10.1007/S10822-017-0070-1},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KayasthaKHVB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Kitchen17,
author = {Douglas B. Kitchen},
title = {Computer-aided drug discovery research at a global contract research
organization},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {309--318},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9991-3},
doi = {10.1007/S10822-016-9991-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Kitchen17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KordopatiTTTGST17,
author = {Golfo G. Kordopati and
Haralambos Tzoupis and
Anastassios N. Troganis and
Gerasimos M. Tsivgoulis and
Simona Golic Grdadolnik and
Carmen Simal and
Theodore V. Tselios},
title = {Biologically relevant conformational features of linear and cyclic
proteolipid protein {(PLP)} peptide analogues obtained by high-resolution
nuclear magnetic resonance and molecular dynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {841--854},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0045-2},
doi = {10.1007/S10822-017-0045-2},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KordopatiTTTGST17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KunimotoB17,
author = {Ryo Kunimoto and
J{\"{u}}rgen Bajorath},
title = {Exploring sets of molecules from patents and relationships to other
active compounds in chemical space networks},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {779--788},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0061-2},
doi = {10.1007/S10822-017-0061-2},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KunimotoB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LalooLRR17,
author = {Jalal Z. A. Laloo and
Nassirah Laloo and
Lydia Rhyman and
Ponnadurai Ramasami},
title = {ExcelAutomat: a tool for systematic processing of files as applied
to quantum chemical calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {667--673},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0031-8},
doi = {10.1007/S10822-017-0031-8},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LalooLRR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LeeTPKHDBSB17,
author = {Juyong Lee and
Florentina Tofoleanu and
Frank C. Pickard IV and
Gerhard K{\"{o}}nig and
Jing Huang and
Ana Damjanovic and
Minkyung Baek and
Chaok Seok and
Bernard R. Brooks},
title = {Absolute binding free energy calculations of CBClip host-guest systems
in the {SAMPL5} blind challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {71--85},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9968-2},
doi = {10.1007/S10822-016-9968-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LeeTPKHDBSB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiWJZZCTLHY17,
author = {Lanlan Li and
Wei Wei and
Wen{-}Juan Jia and
Yongchang Zhu and
Yan Zhang and
Jiang{-}Huai Chen and
Jiaqi Tian and
Huanxiang Liu and
Yong{-}Xing He and
Xiaojun Yao},
title = {Discovery of small molecules binding to the normal conformation of
prion by combining virtual screening and multiple biological activity
evaluation methods},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {12},
pages = {1053--1062},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0086-6},
doi = {10.1007/S10822-017-0086-6},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiWJZZCTLHY17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuWK17,
author = {Kai Liu and
Etsurou Watanabe and
Hironori Kokubo},
title = {Exploring the stability of ligand binding modes to proteins by molecular
dynamics simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {2},
pages = {201--211},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0005-2},
doi = {10.1007/S10822-016-0005-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiuWK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LutyR17,
author = {Brock A. Luty and
Peter W. Rose},
title = {The need for scientific software engineering in the pharmaceutical
industry},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {301--304},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9997-x},
doi = {10.1007/S10822-016-9997-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LutyR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ManasG17,
author = {Eric S. Manas and
Darren V. S. Green},
title = {{CADD} medicine: design is the potion that can cure my disease},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {249--253},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0004-3},
doi = {10.1007/S10822-016-0004-3},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ManasG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Marmolejo-Valencia17,
author = {Andr{\'{e}}s F. Marmolejo{-}Valencia and
Karina Mart{\'{\i}}nez{-}Mayorga},
title = {Allosteric modulation model of the mu opioid receptor by herkinorin,
a potent not alkaloidal agonist},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {5},
pages = {467--482},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0016-7},
doi = {10.1007/S10822-017-0016-7},
timestamp = {Wed, 17 Nov 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Marmolejo-Valencia17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MartinhoSFBBZ17,
author = {Nuno Martinho and
Liana C. Silva and
Helena F. Florindo and
Steve Brocchini and
Teresa S. Barata and
Mire Zloh},
title = {Practical computational toolkits for dendrimers and dendrons structure
design},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {817--827},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0041-6},
doi = {10.1007/S10822-017-0041-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MartinhoSFBBZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/McGaugheyW17,
author = {Georgia B. McGaughey and
W. Patrick Walters},
title = {Modeling {\&} Informatics at Vertex Pharmaceuticals Incorporated:
our philosophy for sustained impact},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {293--300},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9994-0},
doi = {10.1007/S10822-016-9994-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/McGaugheyW17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MishraSAMSKCSSP17,
author = {Arjun K. Mishra and
Nidhi Singh and
Pragati Agnihotri and
Shikha Mishra and
Saurabh P. Singh and
Bala K. Kolli and
Kwang Poo Chang and
Amogh A. Sahasrabuddhe and
Mohammad Imran Siddiqi and
J. Venkatesh Pratap},
title = {Discovery of novel inhibitors for Leishmania nucleoside diphosphatase
kinase {(NDK)} based on its structural and functional characterization},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {6},
pages = {547--562},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0022-9},
doi = {10.1007/S10822-017-0022-9},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/MishraSAMSKCSSP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MueggeBK17,
author = {Ingo Muegge and
Andreas Bergner and
Jan M. Kriegl},
title = {Computer-aided drug design at Boehringer Ingelheim},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {275--285},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9975-3},
doi = {10.1007/S10822-016-9975-3},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MueggeBK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MuzioTP17,
author = {Elena Di Muzio and
Daniele Toti and
Fabio Polticelli},
title = {DockingApp: a user friendly interface for facilitated docking simulations
with AutoDock Vina},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {2},
pages = {213--218},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-0006-1},
doi = {10.1007/S10822-016-0006-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MuzioTP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NguyenJR17,
author = {Minh Khoa Nguyen and
L{\'{e}}onard Jaillet and
St{\'{e}}phane Redon},
title = {As-Rigid-As-Possible molecular interpolation paths},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {403--417},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0012-y},
doi = {10.1007/S10822-017-0012-Y},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NguyenJR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OliveiraAH17,
author = {Edson R. A. Oliveira and
Ricardo B. de Alencastro and
Bruno A. C. Horta},
title = {New insights into flavivirus biology: the influence of pH over interactions
between prM and {E} proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {1009--1019},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0076-8},
doi = {10.1007/S10822-017-0076-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OliveiraAH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PalHKFXLTWKG17,
author = {Rajat Kumar Pal and
Kamran Haider and
Divya Kaur and
William F. Flynn and
Junchao Xia and
Ronald M. Levy and
Tetiana Taran and
Lauren Wickstrom and
Tom Kurtzman and
Emilio Gallicchio},
title = {A combined treatment of hydration and dynamical effects for the modeling
of host-guest binding thermodynamics: the {SAMPL5} blinded challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {29--44},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9956-6},
doi = {10.1007/S10822-016-9956-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PalHKFXLTWKG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PalHKFXLTWKG17a,
author = {Rajat Kumar Pal and
Kamran Haider and
Divya Kaur and
William F. Flynn and
Junchao Xia and
Ronald M. Levy and
Tetiana Taran and
Lauren Wickstrom and
Tom Kurtzman and
Emilio Gallicchio},
title = {Erratum to: {A} combined treatment of hydration and dynamical effects
for the modeling of host-guest binding thermodynamics: the {SAMPL5}
blinded challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {45},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9987-z},
doi = {10.1007/S10822-016-9987-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PalHKFXLTWKG17a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParkHKVLJSMLSKN17,
author = {Insun Park and
Yu Jin Hwang and
TaeHun Kim and
Ambily Nath Indu Viswanath and
Ashwini M. Londhe and
Seo Yun Jung and
Kyoung Mi Sim and
Sun{-}Joon Min and
Ji Eun Lee and
Jihye Seong and
Yun Kyung Kim and
Kyoung Tai No and
Hoon Ryu and
Ae Nim Pae},
title = {In silico probing and biological evaluation of SETDB1/ESET-targeted
novel compounds that reduce tri-methylated histone {H3K9} (H3K9me3)
level},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {877--889},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0052-3},
doi = {10.1007/S10822-017-0052-3},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ParkHKVLJSMLSKN17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParkLKLK17,
author = {Hwangseo Park and
Hye Seon Lee and
Bonsu Ku and
Sang{-}Rae Lee and
Seung Jun Kim},
title = {Two-track virtual screening approach to identify both competitive
and allosteric inhibitors of human small C-terminal domain phosphatase
1},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {743--753},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0037-2},
doi = {10.1007/S10822-017-0037-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ParkLKLK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParkLLPJLLNLP17,
author = {Insun Park and
Ashwini M. Londhe and
Ji Woong Lim and
Beoung{-}Geon Park and
Seo Yun Jung and
Jae Yeol Lee and
Sang Min Lim and
Kyoung Tai No and
Jiyoun Lee and
Ae Nim Pae},
title = {Discovery of non-peptidic small molecule inhibitors of cyclophilin
{D} as neuroprotective agents in A{\(\beta\)}-induced mitochondrial
dysfunction},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {929--941},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0067-9},
doi = {10.1007/S10822-017-0067-9},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ParkLLPJLLNLP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PolishchukMGBNV17,
author = {Pavel G. Polishchuk and
Timur I. Madzhidov and
Timur Gimadiev and
Andrey Bodrov and
Ramil I. Nugmanov and
Alexandre Varnek},
title = {Structure-reactivity modeling using mixture-based representation of
chemical reactions},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {829--839},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0044-3},
doi = {10.1007/S10822-017-0044-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PolishchukMGBNV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RichaISEK17,
author = {Tambi Richa and
Soichiro Ide and
Ryosuke Suzuki and
Teppei Ebina and
Yutaka Kuroda},
title = {Fast {H-DROP:} {A} thirty times accelerated version of {H-DROP} for
interactive SVM-based prediction of helical domain linkers},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {2},
pages = {237--244},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9999-8},
doi = {10.1007/S10822-016-9999-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RichaISEK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SamantaM17,
author = {Sudipta Samanta and
Sanchita Mukherjee},
title = {Co-operative intra-protein structural response due to protein-protein
complexation revealed through thermodynamic quantification: study
of MDM2-p53 binding},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {891--903},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0057-y},
doi = {10.1007/S10822-017-0057-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SamantaM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Sanchez-MurciaC17,
author = {Pedro A. S{\'{a}}nchez{-}Murcia and
{\'{A}}lvaro Cort{\'{e}}s Cabrera and
Federico Gago},
title = {Structural rationale for the cross-resistance of tumor cells bearing
the {A399V} variant of elongation factor eEF1A1 to the structurally
unrelated didemnin B, ternatin, nannocystin {A} and ansatrienin {B}},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {915--928},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0066-x},
doi = {10.1007/S10822-017-0066-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Sanchez-MurciaC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SarramiYK17,
author = {Farzaneh Sarrami and
Li{-}Juan Yu and
Amir Karton},
title = {Computational design of bio-inspired carnosine-based HOBr antioxidants},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {10},
pages = {905--913},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0060-3},
doi = {10.1007/S10822-017-0060-3},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SarramiYK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SchaftenaarVV17,
author = {Gijs Schaftenaar and
Elias Vlieg and
Gert Vriend},
title = {Molden 2.0: quantum chemistry meets proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {789--800},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0042-5},
doi = {10.1007/S10822-017-0042-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SchaftenaarVV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ShirtsKSYGMCZ17,
author = {Michael R. Shirts and
Christoph Klein and
Jason M. Swails and
Jian Yin and
Michael K. Gilson and
David L. Mobley and
David A. Case and
Ellen D. Zhong},
title = {Lessons learned from comparing molecular dynamics engines on the {SAMPL5}
dataset},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {147--161},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9977-1},
doi = {10.1007/S10822-016-9977-1},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ShirtsKSYGMCZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ShirtsKSYGMCZ17a,
author = {Michael R. Shirts and
Christoph Klein and
Jason M. Swails and
Jian Yin and
Michael K. Gilson and
David L. Mobley and
David A. Case and
Ellen D. Zhong},
title = {Erratum to: Lessons learned from comparing molecular dynamics engines
on the {SAMPL5} dataset},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {777},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0043-4},
doi = {10.1007/S10822-017-0043-4},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ShirtsKSYGMCZ17a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SidorovVDMMHV17,
author = {Pavel Sidorov and
Birgit Viira and
Elisabeth Davioud{-}Charvet and
Uko Maran and
Gilles Marcou and
Dragos Horvath and
Alexandre Varnek},
title = {{QSAR} modeling and chemical space analysis of antimalarial compounds},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {5},
pages = {441--451},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0019-4},
doi = {10.1007/S10822-017-0019-4},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SidorovVDMMHV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SmallALHM17,
author = {Meagan C. Small and
Asaminew H. Aytenfisu and
Fang{-}Yu Lin and
Xibing He and
Alexander D. MacKerell Jr.},
title = {Drude polarizable force field for aliphatic ketones and aldehydes,
and their associated acyclic carbohydrates},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {4},
pages = {349--363},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0010-0},
doi = {10.1007/S10822-017-0010-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SmallALHM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SouzaOA17,
author = {Anacleto Silva de Souza and
Marcelo T. de Oliveira and
Adriano D. Andricopulo},
title = {Development of a pharmacophore for cruzain using oxadiazoles as virtual
molecular probes: quantitative structure-activity relationship studies},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {9},
pages = {801--816},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0039-0},
doi = {10.1007/S10822-017-0039-0},
timestamp = {Wed, 08 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SouzaOA17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/St-GallayS17,
author = {Stephen A. St{-}Gallay and
Colin P. Sambrook{-}Smith},
title = {Tools, techniques, organisation and culture of the {CADD} group at
Sygnature Discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {305--308},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9989-x},
doi = {10.1007/S10822-016-9989-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/St-GallayS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/StawoskaDWJSSS17,
author = {Iwona Stawoska and
A. Dudzik and
M. Wasylewski and
M. Jemiola{-}Rzeminska and
Andrzej Skoczowski and
K. Strzalka and
Maciej Szaleniec},
title = {DFT-based prediction of reactivity of short-chain alcohol dehydrogenase},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {6},
pages = {587--602},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0026-5},
doi = {10.1007/S10822-017-0026-5},
timestamp = {Fri, 06 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/StawoskaDWJSSS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Stouch17,
author = {Terry R. Stouch},
title = {Urgency and austerity as drivers of success},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {329--334},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0018-5},
doi = {10.1007/S10822-017-0018-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Stouch17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SullivanSNDG17,
author = {Matthew R. Sullivan and
Punidha Sokkalingam and
Thong Nguyen and
James P. Donahue and
Bruce C. Gibb},
title = {Binding of carboxylate and trimethylammonium salts to octa-acid and
{TEMOA} deep-cavity cavitands},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {21--28},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9925-0},
doi = {10.1007/S10822-016-9925-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SullivanSNDG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TofoleanuLPKHBS17,
author = {Florentina Tofoleanu and
Juyong Lee and
Frank C. Pickard IV and
Gerhard K{\"{o}}nig and
Jing Huang and
Minkyung Baek and
Chaok Seok and
Bernard R. Brooks},
title = {Absolute binding free energies for octa-acids and guests in {SAMPL5}
- Evaluating binding free energies for octa-acid and guest complexes
in the {SAMPL5} blind challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {107--118},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9965-5},
doi = {10.1007/S10822-016-9965-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TofoleanuLPKHBS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TsuiOB17,
author = {Vickie Tsui and
Daniel F. Ortwine and
Jeffrey M. Blaney},
title = {Enabling drug discovery project decisions with integrated computational
chemistry and informatics},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {287--291},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9988-y},
doi = {10.1007/S10822-016-9988-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TsuiOB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Tsuji17,
author = {Motonori Tsuji},
title = {Antagonist-perturbation mechanism for activation function-2 fixed
motifs: active conformation and docking mode of retinoid {X} receptor
antagonists},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {6},
pages = {577--585},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0025-6},
doi = {10.1007/S10822-017-0025-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Tsuji17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VlijmenDM17,
author = {Herman van Vlijmen and
Renee L. DesJarlais and
Tara Mirzadegan},
title = {Computational chemistry at Janssen},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {267--273},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9998-9},
doi = {10.1007/S10822-016-9998-9},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VlijmenDM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WangGPL17,
author = {Yu Wang and
Yanzhi Guo and
Xuemei Pu and
Menglong Li},
title = {Effective prediction of bacterial type {IV} secreted effectors by
combined features of both C-termini and N-termini},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {11},
pages = {1029--1038},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0080-z},
doi = {10.1007/S10822-017-0080-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WangGPL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Warr17,
author = {Wendy A. Warr},
title = {A CADD-alog of strategies in pharma},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {3},
pages = {245--247},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0017-6},
doi = {10.1007/S10822-017-0017-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Warr17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WestermaierRTPP17,
author = {Yvonne Westermaier and
Sergio Ruiz{-}Carmona and
Isabelle Theret and
Fran{\c{c}}oise Perron{-}Sierra and
Guillaume Poissonnet and
Catherine Dacquet and
Jean A. Boutin and
Pierre Ducrot and
Xavier Barril},
title = {Binding mode prediction and MD/MMPBSA-based free energy ranking for
agonists of REV-ERB{\(\alpha\)}/NCoR},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {755--775},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0040-7},
doi = {10.1007/S10822-017-0040-7},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WestermaierRTPP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/XuYZ17,
author = {Xianjin Xu and
Chengfei Yan and
Xiaoqin Zou},
title = {Improving binding mode and binding affinity predictions of docking
by ligand-based search of protein conformations: evaluation in {D3R}
grand challenge 2015},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {8},
pages = {689--699},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0038-1},
doi = {10.1007/S10822-017-0038-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/XuYZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YinHSG17,
author = {Jian Yin and
Niel M. Henriksen and
David R. Slochower and
Michael K. Gilson},
title = {The {SAMPL5} host-guest challenge: computing binding free energies
and enthalpies from explicit solvent simulations by the attach-pull-release
{(APR)} method},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {133--145},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9970-8},
doi = {10.1007/S10822-016-9970-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YinHSG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YinHSSCMG17,
author = {Jian Yin and
Niel M. Henriksen and
David R. Slochower and
Michael R. Shirts and
Michael Chiu and
David L. Mobley and
Michael K. Gilson},
title = {Overview adcm43.bhtof the {SAMPL5} host-guest challenge: Are we doing
better?},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {1},
pages = {1--19},
year = {2017},
url = {https://doi.org/10.1007/s10822-016-9974-4},
doi = {10.1007/S10822-016-9974-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YinHSSCMG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YunKK17,
author = {Giseok Yun and
Jaehoon Kim and
Do{-}Nyun Kim},
title = {A critical assessment of finite element modeling approach for protein
dynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {609--624},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0027-4},
doi = {10.1007/S10822-017-0027-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YunKK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZauggGMB17,
author = {Julian Zaugg and
Yosephine Gumulya and
Alpeshkumar K. Malde and
Mikael Bod{\'{e}}n},
title = {Learning epistatic interactions from sequence-activity data to predict
enantioselectivity},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {12},
pages = {1085--1096},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0090-x},
doi = {10.1007/S10822-017-0090-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZauggGMB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZunigaAJJ17,
author = {Mat{\'{\i}}as A. Z{\'{u}}{\~{n}}iga and
Joel B. Alderete and
Gonzalo A. Ja{\~{n}}a and
Ver{\'{o}}nica A. Jim{\'{e}}nez},
title = {Structural insight into the role of Gln293Met mutation on the Peloruside
A/Laulimalide association with {\(\alpha\)}{\(\beta\)}-tubulin from
molecular dynamics simulations, binding free energy calculations and
weak interactions analysis},
journal = {J. Comput. Aided Mol. Des.},
volume = {31},
number = {7},
pages = {643--652},
year = {2017},
url = {https://doi.org/10.1007/s10822-017-0029-2},
doi = {10.1007/S10822-017-0029-2},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZunigaAJJ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/0001Z16,
author = {Ashutosh Kumar and
Kam Y. J. Zhang},
title = {A pose prediction approach based on ligand 3D shape similarity},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {6},
pages = {457--469},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9923-2},
doi = {10.1007/S10822-016-9923-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/0001Z16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AlbercaSBFCMBCT16,
author = {Lucas N. Alberca and
Mar{\'{\i}}a L. Sbaraglini and
Dar{\'{\i}}o E. Balcazar and
Laura Fraccaroli and
Carolina Carrillo and
Andrea Medeiros and
Diego Benitez and
Marcelo A. Comini and
Alan Talevi},
title = {Discovery of novel polyamine analogs with anti-protozoal activity
by computer guided drug repositioning},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {4},
pages = {305--321},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9903-6},
doi = {10.1007/S10822-016-9903-6},
timestamp = {Thu, 14 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AlbercaSBFCMBCT16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AlmeidaLMGMSB16,
author = {Hugo de Almeida and
Vincent Leroux and
Fl{\'{a}}via Nader Motta and
Philippe Grellier and
Bernard Maigret and
Jaime Martins Santana and
Izabela Marques Dourado Bastos},
title = {Identification of novel \emph{Trypanosoma cruzi} prolyl oligopeptidase
inhibitors by structure-based virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {12},
pages = {1165--1174},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9985-1},
doi = {10.1007/S10822-016-9985-1},
timestamp = {Thu, 18 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AlmeidaLMGMSB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AnighoroB16,
author = {Andrew Anighoro and
J{\"{u}}rgen Bajorath},
title = {Binding mode similarity measures for ranking of docking poses: a case
study on the adenosine {A2A} receptor},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {6},
pages = {447--456},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9918-z},
doi = {10.1007/S10822-016-9918-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AnighoroB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AnighoroLB16,
author = {Andrew Anighoro and
Antonio de la Vega de Le{\'{o}}n and
J{\"{u}}rgen Bajorath},
title = {Predicting bioactive conformations and binding modes of macrocycles},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {10},
pages = {841--849},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9973-5},
doi = {10.1007/S10822-016-9973-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AnighoroLB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ArroyueloVM16,
author = {Agustina Arroyuelo and
Jorge A. Vila and
Osvaldo A. Martin},
title = {Azahar: a PyMOL plugin for construction, visualization and analysis
of glycan molecules},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {8},
pages = {619--624},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9944-x},
doi = {10.1007/S10822-016-9944-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ArroyueloVM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BaltoumasTH16,
author = {Fotis A. Baltoumas and
Margarita C. Theodoropoulou and
Stavros J. Hamodrakas},
title = {Molecular dynamics simulations and structure-based network analysis
reveal structural and functional aspects of G-protein coupled receptor
dimer interactions},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {6},
pages = {489--512},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9919-y},
doi = {10.1007/S10822-016-9919-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BaltoumasTH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BannanBCSGM16,
author = {Caitlin C. Bannan and
Kalistyn H. Burley and
Michael Chiu and
Michael R. Shirts and
Michael K. Gilson and
David L. Mobley},
title = {Blind prediction of cyclohexane-water distribution coefficients from
the {SAMPL5} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {927--944},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9954-8},
doi = {10.1007/S10822-016-9954-8},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/BannanBCSGM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BednarkoWSLN16,
author = {Justyna Bednarko and
Justyna Wielinska and
Karol Sikora and
Beata Liberek and
Andrzej Nowacki},
title = {Theoretical studies on the reaction of mono- and ditriflate derivatives
of 1, 4: 3, 6-dianhydro-d-mannitol with trimethylamine - Can a quaternary
ammonium salt be a source of the methyl group?},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {1},
pages = {13--26},
year = {2016},
url = {https://doi.org/10.1007/s10822-015-9885-9},
doi = {10.1007/S10822-015-9885-9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BednarkoWSLN16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BehrenBNR16,
author = {Mathias M. von Behren and
Stefan Bietz and
Eva Nittinger and
Matthias Rarey},
title = {mRAISE: an alternative algorithmic approach to ligand-based virtual
screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {8},
pages = {583--594},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9940-1},
doi = {10.1007/S10822-016-9940-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BehrenBNR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BosisioMM16,
author = {Stefano Bosisio and
Antonia S. J. S. Mey and
Julien Michel},
title = {Blinded predictions of distribution coefficients in the {SAMPL5} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {1101--1114},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9969-1},
doi = {10.1007/S10822-016-9969-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BosisioMM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BriniPFD16,
author = {Emiliano Brini and
S. Shanaka Paranahewage and
Christopher J. Fennell and
Ken A. Dill},
title = {Adapting the semi-explicit assembly solvation model for estimating
water-cyclohexane partitioning with the {SAMPL5} molecules},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {1067--1077},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9961-9},
doi = {10.1007/S10822-016-9961-9},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/BriniPFD16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CardoneBSPH16,
author = {Antonio Cardone and
Mary Brady and
Ram D. Sriram and
Harish C. Pant and
Sergio A. Hassan},
title = {Computational study of the inhibitory mechanism of the kinase {CDK5}
hyperactivity by peptide p5 and derivation of a pharmacophore},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {6},
pages = {513--521},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9922-3},
doi = {10.1007/S10822-016-9922-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CardoneBSPH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChavanAWN16,
author = {Swapnil Chavan and
Ahmed Abdelaziz and
Jesper G. Wiklander and
Ian A. Nicholls},
title = {A k-nearest neighbor classification of hERG {K+} channel blockers},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {3},
pages = {229--236},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9898-z},
doi = {10.1007/S10822-016-9898-Z},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ChavanAWN16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChoSKSJSSLLKNP16,
author = {Nam{-}Chul Cho and
Seoung{-}Hwan Seo and
Dohee Kim and
Ji{-}Sun Shin and
Jeongmin Ju and
Jihye Seong and
Seon Hee Seo and
Iiyoun Lee and
Kyung{-}Tae Lee and
Yun Kyung Kim and
Kyoung Tai No and
Ae Nim Pae},
title = {Pharmacophore-based virtual screening, biological evaluation and binding
mode analysis of a novel protease-activated receptor 2 antagonist},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {8},
pages = {625--637},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9937-9},
doi = {10.1007/S10822-016-9937-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChoSKSJSSLLKNP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChungP16,
author = {Kee{-}Choo Chung and
Hwangseo Park},
title = {Extended solvent-contact model approach to blind {SAMPL5} prediction
challenge for the distribution coefficients of drug-like molecules},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {1019--1033},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9928-x},
doi = {10.1007/S10822-016-9928-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChungP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ClevesJ16,
author = {Ann E. Cleves and
Ajay N. Jain},
title = {Extrapolative prediction using physically-based {QSAR}},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {2},
pages = {127--152},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9896-1},
doi = {10.1007/S10822-016-9896-1},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ClevesJ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DengFXVZHMGL16,
author = {Nan{-}Jie Deng and
William F. Flynn and
Junchao Xia and
R. S. K. Vijayan and
Baofeng Zhang and
Peng He and
Ahmet Mentes and
Emilio Gallicchio and
Ronald M. Levy},
title = {Large scale free energy calculations for blind predictions of protein-ligand
binding: the {D3R} Grand Challenge 2015},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {743--751},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9952-x},
doi = {10.1007/S10822-016-9952-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DengFXVZHMGL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Diaz-RodriguezB16,
author = {Sebastian Diaz{-}Rodriguez and
Samantha M. Bozada and
Jeremy R. Phifer and
Andrew S. Paluch},
title = {Predicting cyclohexane/water distribution coefficients for the {SAMPL5}
challenge using {MOSCED} and the {SMD} solvation model},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {1007--1017},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9945-9},
doi = {10.1007/S10822-016-9945-9},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Diaz-RodriguezB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DidziapetrisL16,
author = {Remigijus Didziapetris and
Kiril Lanevskij},
title = {Compilation and physicochemical classification analysis of a diverse
hERG inhibition database},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {12},
pages = {1175--1188},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9986-0},
doi = {10.1007/S10822-016-9986-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DidziapetrisL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Garrido-Arandia16,
author = {Mar{\'{\i}}a Garrido{-}Arandia and
Jorge Bretones and
Cristina G{\'{o}}mez{-}Casado and
Nuria Cubells and
Araceli D{\'{\i}}az{-}Perales and
Luis Fern{\'{a}}ndez Pacios},
title = {Computational study of pH-dependent oligomerization and ligand binding
in Alt a 1, a highly allergenic protein with a unique fold},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {5},
pages = {365--379},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9911-6},
doi = {10.1007/S10822-016-9911-6},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Garrido-Arandia16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GathiakaLCYSKDK16,
author = {Symon Gathiaka and
Shuai Liu and
Michael Chiu and
Huanwang Yang and
Jeanne A. Stuckey and
You{-}Na Kang and
Jim Delproposto and
Ginger Kubish and
James B. Dunbar Jr. and
Heather A. Carlson and
Stephen K. Burley and
W. Patrick Walters and
Rommie E. Amaro and
Victoria A. Feher and
Michael K. Gilson},
title = {{D3R} grand challenge 2015: Evaluation of protein-ligand pose and
affinity predictions},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {651--668},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9946-8},
doi = {10.1007/S10822-016-9946-8},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GathiakaLCYSKDK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GenhedenE16,
author = {Samuel Genheden and
Jonathan W. Essex},
title = {All-atom/coarse-grained hybrid predictions of distribution coefficients
in {SAMPL5}},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {969--976},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9926-z},
doi = {10.1007/S10822-016-9926-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GenhedenE16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GiantiMLZ16,
author = {Eleonora Gianti and
Troy E. Messick and
Paul M. Lieberman and
Randy J. Zauhar},
title = {Computational analysis of {EBNA1} "druggability" suggests novel insights
for Epstein-Barr virus inhibitor design},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {4},
pages = {285--303},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9899-y},
doi = {10.1007/S10822-016-9899-Y},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GiantiMLZ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GrudininKEMC16,
author = {Sergei Grudinin and
Maria Kadukova and
Andreas Eisenbarth and
Simon Marillet and
Fr{\'{e}}d{\'{e}}ric Cazals},
title = {Predicting binding poses and affinities for protein - ligand complexes
in the 2015 {D3R} Grand Challenge using a physical model with a statistical
parameter estimation},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {791--804},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9976-2},
doi = {10.1007/S10822-016-9976-2},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GrudininKEMC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HatmalJT16,
author = {M{\'{a}}mon M. Hatmal and
Shadi Jaber and
Mutasem O. Taha},
title = {Combining molecular dynamics simulation and ligand-receptor contacts
analysis as a new approach for pharmacophore modeling: beta-secretase
1 and check point kinase 1 as case studies},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {12},
pages = {1149--1163},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9984-2},
doi = {10.1007/S10822-016-9984-2},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/HatmalJT16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HuSLCYG16,
author = {Yuan Hu and
Brad Sherborne and
Tai{-}Sung Lee and
David A. Case and
Darrin M. York and
Zhuyan Guo},
title = {The importance of protonation and tautomerization in relative binding
affinity prediction: a comparison of {AMBER} {TI} and Schr{\"{o}}dinger
{FEP}},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {7},
pages = {533--539},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9920-5},
doi = {10.1007/S10822-016-9920-5},
timestamp = {Sat, 30 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/HuSLCYG16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/IgnjatovicCDMAR16,
author = {Majda Misini Ignjatovic and
Octav Caldararu and
Geng Dong and
Camila Mu{\~{n}}oz{-}Guti{\'{e}}rrez and
Francisco Adasme{-}Carre{\~{n}}o and
Ulf Ryde},
title = {Binding-affinity predictions of {HSP90} in the {D3R} Grand Challenge
2015 with docking, MM/GBSA, QM/MM, and free-energy simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {707--730},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9942-z},
doi = {10.1007/S10822-016-9942-Z},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/IgnjatovicCDMAR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Ishikawa16,
author = {Takeshi Ishikawa},
title = {Prediction of peptide binding to a major histocompatibility complex
class {I} molecule based on docking simulation},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {10},
pages = {875--887},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9967-3},
doi = {10.1007/S10822-016-9967-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Ishikawa16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JaghooriBO16,
author = {Mohammad Mahdi Jaghoori and
Boris Bleijlevens and
S{\'{\i}}lvia Delgado Olabarriaga},
title = {1001 Ways to run AutoDock Vina for virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {3},
pages = {237--249},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9900-9},
doi = {10.1007/S10822-016-9900-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/JaghooriBO16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JonesBW16,
author = {Michael R. Jones and
Bernard R. Brooks and
Angela K. Wilson},
title = {Partition coefficients for the {SAMPL5} challenge using transfer free
energies},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {1129--1138},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9964-6},
doi = {10.1007/S10822-016-9964-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/JonesBW16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KamathKFLIBOP16,
author = {Ganesh Kamath and
Igor Kurnikov and
Boris Fain and
Igor V. Leontyev and
Alexey A. Illarionov and
Oleg Butin and
Michael A. Olevanov and
Leonid B. Pereyaslavets},
title = {Prediction of cyclohexane-water distribution coefficient for {SAMPL5}
drug-like compounds with the {QMPFF3} and {ARROW} polarizable force
fields},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {977--988},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9958-4},
doi = {10.1007/S10822-016-9958-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KamathKFLIBOP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KearnesMBPR16,
author = {Steven Kearnes and
Kevin McCloskey and
Marc Berndl and
Vijay S. Pande and
Patrick Riley},
title = {Molecular graph convolutions: moving beyond fingerprints},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {8},
pages = {595--608},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9938-8},
doi = {10.1007/S10822-016-9938-8},
timestamp = {Wed, 20 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KearnesMBPR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KearnesP16,
author = {Steven Kearnes and
Vijay S. Pande},
title = {ROCS-derived features for virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {8},
pages = {609--617},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9959-3},
doi = {10.1007/S10822-016-9959-3},
timestamp = {Wed, 20 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KearnesP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KenneyBI16,
author = {Ian M. Kenney and
Oliver Beckstein and
Bogdan I. Iorga},
title = {Prediction of cyclohexane-water distribution coefficients for the
{SAMPL5} data set using molecular dynamics simulations with the {OPLS-AA}
force field},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {1045--1058},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9949-5},
doi = {10.1007/S10822-016-9949-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KenneyBI16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KlamtERW16,
author = {Andreas Klamt and
Frank Eckert and
Jens Reinisch and
Karin Wichmann},
title = {Prediction of cyclohexane-water distribution coefficients with {COSMO-RS}
on the {SAMPL5} data set},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {959--967},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9927-y},
doi = {10.1007/S10822-016-9927-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KlamtERW16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KonigPHSTLDPJST16,
author = {Gerhard K{\"{o}}nig and
Frank C. Pickard IV and
Jing Huang and
Andrew C. Simmonett and
Florentina Tofoleanu and
Juyong Lee and
Pavlo O. Dral and
Samarjeet Prasad and
Michael R. Jones and
Yihan Shao and
Walter Thiel and
Bernard R. Brooks},
title = {Calculating distribution coefficients based on multi-scale free energy
simulations: an evaluation of {MM} and {QM/MM} explicit solvent simulations
of water-cyclohexane transfer in the {SAMPL5} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {989--1006},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9936-x},
doi = {10.1007/S10822-016-9936-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KonigPHSTLDPJST16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KulshreshthaCGM16,
author = {Shweta Kulshreshtha and
Vigi Chaudhary and
Girish K. Goswami and
Nidhi Mathur},
title = {Computational approaches for predicting mutant protein stability},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {5},
pages = {401--412},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9914-3},
doi = {10.1007/S10822-016-9914-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KulshreshthaCGM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KumarZ16,
author = {Ashutosh Kumar and
Kam Y. J. Zhang},
title = {Prospective evaluation of shape similarity based pose prediction method
in {D3R} Grand Challenge 2015},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {685--693},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9931-2},
doi = {10.1007/S10822-016-9931-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KumarZ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KunimotoVB16,
author = {Ryo Kunimoto and
Martin Vogt and
J{\"{u}}rgen Bajorath},
title = {Maximum common substructure-based Tversky index: an asymmetric hybrid
similarity measure},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {7},
pages = {523--531},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9935-y},
doi = {10.1007/S10822-016-9935-Y},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KunimotoVB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LearC16,
author = {Sam Lear and
Steven L. Cobb},
title = {Pep-Calc.com: a set of web utilities for the calculation of peptide
and peptoid properties and automatic mass spectral peak assignment},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {3},
pages = {271--277},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9902-7},
doi = {10.1007/S10822-016-9902-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LearC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LeeB16,
author = {Sehan Lee and
Mace G. Barron},
title = {A mechanism-based 3D-QSAR approach for classification and prediction
of acetylcholinesterase inhibitory potency of organophosphate and
carbamate analogs},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {4},
pages = {347--363},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9910-7},
doi = {10.1007/S10822-016-9910-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LeeB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LenselinkBVMSVI16,
author = {Eelke B. Lenselink and
Thijs Beuming and
Corine van Veen and
Arnault Massink and
Woody Sherman and
Herman W. T. van Vlijmen and
Adriaan P. IJzerman},
title = {In search of novel ligands using a structure-based approach: a case
study on the adenosine {A2A} receptor},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {10},
pages = {863--874},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9963-7},
doi = {10.1007/S10822-016-9963-7},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LenselinkBVMSVI16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiF16,
author = {Juan Li and
Huisheng Fang},
title = {A comparison of different functions for predicted protein model quality
assessment},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {7},
pages = {553--558},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9924-1},
doi = {10.1007/S10822-016-9924-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuHLLZ16,
author = {Hongli Liu and
Rui Han and
Jiazhong Li and
Huanxiang Liu and
Lifang Zheng},
title = {Molecular mechanism of R-bicalutamide switching from androgen receptor
antagonist to agonist induced by amino acid mutations using molecular
dynamics simulations and free energy calculation},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {12},
pages = {1189--1200},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9992-2},
doi = {10.1007/S10822-016-9992-2},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiuHLLZ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LoefflerEFL16,
author = {Johannes R. Loeffler and
Emanuel S. R. Ehmki and
Julian E. Fuchs and
Klaus R. Liedl},
title = {Kinetic barriers in the isomerization of substituted ureas: implications
for computer-aided drug design},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {5},
pages = {391--400},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9913-4},
doi = {10.1007/S10822-016-9913-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LoefflerEFL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LourosBHI16,
author = {Nikolaos N. Louros and
Fotis A. Baltoumas and
Stavros J. Hamodrakas and
Vassiliki A. Iconomidou},
title = {A {\(\beta\)}-solenoid model of the Pmel17 repeat domain: insights
to the formation of functional amyloid fibrils},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {2},
pages = {153--164},
year = {2016},
url = {https://doi.org/10.1007/s10822-015-9892-x},
doi = {10.1007/S10822-015-9892-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LourosBHI16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LuchkoBLJK16,
author = {Tyler Luchko and
Nikolay Blinov and
Garrett C. Limon and
Kevin P. Joyce and
Andriy Kovalenko},
title = {{SAMPL5:} 3D-RISM partition coefficient calculations with partial
molar volume corrections and solute conformational sampling},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {1115--1127},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9947-7},
doi = {10.1007/S10822-016-9947-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LuchkoBLJK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LuoWHDZ16,
author = {Hua{-}Jun Luo and
Jun{-}Zhi Wang and
Nian{-}Yu Huang and
Wei{-}Qiao Deng and
Kun Zou},
title = {Computational insights into the interaction mechanism of triazolyl
substituted tetrahydrobenzofuran derivatives with H+, K+-ATPase at
different pH},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {1},
pages = {27--37},
year = {2016},
url = {https://doi.org/10.1007/s10822-015-9886-8},
doi = {10.1007/S10822-015-9886-8},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LuoWHDZ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LupalaGP16,
author = {Cecylia S. Lupala and
Patricia G{\'{o}}mez{-}Guti{\'{e}}rrez and
Juan Jes{\'{u}}s P{\'{e}}rez},
title = {New insights into the stereochemical requirements of the bradykinin
{B2} receptor antagonists binding},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {1},
pages = {85--101},
year = {2016},
url = {https://doi.org/10.1007/s10822-015-9890-z},
doi = {10.1007/S10822-015-9890-Z},
timestamp = {Fri, 14 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LupalaGP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MendenhallM16,
author = {Jeffrey L. Mendenhall and
Jens Meiler},
title = {Improving quantitative structure-activity relationship models using
Artificial Neural Networks trained with dropout},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {2},
pages = {177--189},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9895-2},
doi = {10.1007/S10822-016-9895-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MendenhallM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MiyaoKF16,
author = {Tomoyuki Miyao and
Hiromasa Kaneko and
Kimito Funatsu},
title = {Ring system-based chemical graph generation for de novo molecular
design},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {5},
pages = {425--446},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9916-1},
doi = {10.1007/S10822-016-9916-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MiyaoKF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Nicholls16,
author = {Anthony Nicholls},
title = {Confidence limits, error bars and method comparison in molecular modeling.
Part 2: comparing methods},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {2},
pages = {103--126},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9904-5},
doi = {10.1007/S10822-016-9904-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Nicholls16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Nicholls16a,
author = {Anthony Nicholls},
title = {Statistics in molecular modeling: a summary},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {4},
pages = {279--280},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9907-2},
doi = {10.1007/S10822-016-9907-2},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Nicholls16a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OchoaWFMRM16,
author = {Rodrigo Ochoa and
Stanley J. Watowich and
Andr{\'{e}}s F. Fl{\'{o}}rez and
Carol V. Mesa and
Sara M. Robledo and
Carlos Muskus},
title = {Drug search for leishmaniasis: a virtual screening approach by grid
computing},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {7},
pages = {541--552},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9921-4},
doi = {10.1007/S10822-016-9921-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OchoaWFMRM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParanahewageGF16,
author = {S. Shanaka Paranahewage and
Cassidy S. Gierhart and
Christopher J. Fennell},
title = {Predicting water-to-cyclohexane partitioning of the {SAMPL5} molecules
using dielectric balancing of force fields},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {1059--1065},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9950-z},
doi = {10.1007/S10822-016-9950-Z},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ParanahewageGF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PhanichRKH16,
author = {Jiraphorn Phanich and
Thanyada Rungrotmongkol and
Nawee Kungwan and
Supot Hannongbua},
title = {Role of {R292K} mutation in influenza {H7N9} neuraminidase toward
oseltamivir susceptibility: {MD} and {MM/PB(GB)SA} study},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {10},
pages = {917--926},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9981-5},
doi = {10.1007/S10822-016-9981-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PhanichRKH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PiccirilloMSA16,
author = {Erika Piccirillo and
Benjamin Merget and
Christoph A. Sotriffer and
Antonia T. do Amaral},
title = {Conformational flexibility of {DENV} NS2B/NS3pro: from the inhibitor
effect to the serotype influence},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {3},
pages = {251--270},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9901-8},
doi = {10.1007/S10822-016-9901-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PiccirilloMSA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PickardKTLSSPB16,
author = {Frank C. Pickard IV and
Gerhard K{\"{o}}nig and
Florentina Tofoleanu and
Juyong Lee and
Andrew C. Simmonett and
Yihan Shao and
Jay W. Ponder and
Bernard R. Brooks},
title = {Blind prediction of distribution in the {SAMPL5} challenge with {QM}
based protomer and p\emph{K} \({}_{\mbox{a}}\) corrections},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {1087--1100},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9955-7},
doi = {10.1007/S10822-016-9955-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PickardKTLSSPB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PiottoBFPSC16,
author = {Stefano Piotto and
Luigi Di Biasi and
Riccardo Fino and
Raffaele Parisi and
Lucia Sessa and
Simona Concilio},
title = {Yada: a novel tool for molecular docking calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {753--759},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9953-9},
doi = {10.1007/S10822-016-9953-9},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PiottoBFPSC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PolanskiBT16,
author = {Jaroslaw Polanski and
Jacek Bogocz and
Aleksandra Tkocz},
title = {The analysis of the market success of {FDA} approvals by probing top
100 bestselling drugs},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {5},
pages = {381--389},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9912-5},
doi = {10.1007/S10822-016-9912-5},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PolanskiBT16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PrathipatiNAM16,
author = {Philip Prathipati and
Chioko Nagao and
Shandar Ahmad and
Kenji Mizuguchi},
title = {Improved pose and affinity predictions using different protocols tailored
on the basis of data availability},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {817--828},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9982-4},
doi = {10.1007/S10822-016-9982-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PrathipatiNAM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RossokhinZ16,
author = {Alexey V. Rossokhin and
Boris S. Zhorov},
title = {Side chain flexibility and the pore dimensions in the {GABAA} receptor},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {7},
pages = {559--567},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9929-9},
doi = {10.1007/S10822-016-9929-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RossokhinZ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Ruiz-CarmonaB16,
author = {Sergio Ruiz{-}Carmona and
Xavier Barril},
title = {Docking-undocking combination applied to the {D3R} Grand Challenge
2015},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {805--815},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9979-z},
doi = {10.1007/S10822-016-9979-Z},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Ruiz-CarmonaB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RustenburgDLFOM16,
author = {Ari{\"{e}}n S. Rustenburg and
Justin Dancer and
Baiwei Lin and
Jianwen A. Feng and
Daniel F. Ortwine and
David L. Mobley and
John D. Chodera},
title = {Measuring experimental cyclohexane-water distribution coefficients
for the {SAMPL5} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {945--958},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9971-7},
doi = {10.1007/S10822-016-9971-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RustenburgDLFOM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RybinskaSBP16,
author = {Anna Rybinska and
Anita Sosnowska and
Maciej Barycki and
Tomasz Puzyn},
title = {Geometry optimization method versus predictive ability in {QSPR} modeling
for ionic liquids},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {2},
pages = {165--176},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9894-3},
doi = {10.1007/S10822-016-9894-3},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RybinskaSBP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SalmasoSCM16,
author = {Veronica Salmaso and
Mattia Sturlese and
Alberto Cuzzolin and
Stefano Moro},
title = {DockBench as docking selector tool: the lesson learned from {D3R}
Grand Challenge 2015},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {773--789},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9966-4},
doi = {10.1007/S10822-016-9966-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SalmasoSCM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Santos-Martins16,
author = {Diogo Santos{-}Martins},
title = {Interaction with specific {HSP90} residues as a scoring function:
validation in the {D3R} Grand Challenge 2015},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {731--742},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9943-y},
doi = {10.1007/S10822-016-9943-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Santos-Martins16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Santos-MartinsF16,
author = {Diogo Santos{-}Martins and
Pedro Alexandrino Fernandes and
Maria Jo{\~{a}}o Ramos},
title = {Calculation of distribution coefficients in the {SAMPL5} challenge
from atomic solvation parameters and surface areas},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {1079--1086},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9951-y},
doi = {10.1007/S10822-016-9951-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Santos-MartinsF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SelwaMI16,
author = {Edithe Selwa and
Virginie Y. Martiny and
Bogdan I. Iorga},
title = {Molecular docking performance evaluated on the {D3R} Grand Challenge
2015 drug-like ligand datasets},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {829--839},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9983-3},
doi = {10.1007/S10822-016-9983-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SelwaMI16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SercinogluOKO16,
author = {Onur Ser{\c{c}}inoglu and
G{\"{u}}lin {\"{O}}zcan and
Zeynep Kutlu Kabas and
Pemra Ozbek},
title = {A computational docking study on the pH dependence of peptide binding
to {HLA-B27} sub-types differentially associated with ankylosing spondylitis},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {7},
pages = {569--581},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9934-z},
doi = {10.1007/S10822-016-9934-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SercinogluOKO16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SgrignaniLTDDNP16,
author = {Jacopo Sgrignani and
Filomena De Luca and
Hayarpi Torosyan and
Jean{-}Denis Docquier and
Da Duan and
Beatrice Novati and
Fabio Prati and
Giorgio Colombo and
Giovanni Grazioso},
title = {Structure-based approach for identification of novel phenylboronic
acids as serine-{\(\beta\)}-lactamase inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {10},
pages = {851--861},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9962-8},
doi = {10.1007/S10822-016-9962-8},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SgrignaniLTDDNP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ShahinSSAH16,
author = {Rand Shahin and
Lubna Swellmeen and
Omar Shaheen and
Nour Aboalhaija and
Maha Habash},
title = {Identification of novel inhibitors for Pim-1 kinase using pharmacophore
modeling based on a novel method for selecting pharmacophore generation
subsets},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {1},
pages = {39--68},
year = {2016},
url = {https://doi.org/10.1007/s10822-015-9887-7},
doi = {10.1007/S10822-015-9887-7},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ShahinSSAH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SherborneSCCDDL16,
author = {Bradley Sherborne and
Veerabahu Shanmugasundaram and
Alan C. Cheng and
Clara D. Christ and
Renee L. DesJarlais and
Jos{\'{e}} S. Duca and
Richard A. Lewis and
Deborah A. Loughney and
Eric S. Manas and
Georgia B. McGaughey and
Catherine E. Peishoff and
Herman van Vlijmen},
title = {Collaborating to improve the use of free-energy and other quantitative
methods in drug discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {12},
pages = {1139--1141},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9996-y},
doi = {10.1007/S10822-016-9996-Y},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SherborneSCCDDL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SinghBM16,
author = {Bipin Singh and
Gopalakrishnan Bulusu and
Abhijit Mitra},
title = {Effects of point mutations on the thermostability of B. subtilis lipase:
investigating nonadditivity},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {10},
pages = {899--916},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9978-0},
doi = {10.1007/S10822-016-9978-0},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SinghBM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SliwoskiMM16,
author = {Gregory Sliwoski and
Jeffrey L. Mendenhall and
Jens Meiler},
title = {Autocorrelation descriptor improvements for {QSAR:} 2DA{\_}Sign and
3DA{\_}Sign},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {3},
pages = {209--217},
year = {2016},
url = {https://doi.org/10.1007/s10822-015-9893-9},
doi = {10.1007/S10822-015-9893-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SliwoskiMM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SlynkoSBR16,
author = {Inna Slynko and
Franck Da Silva and
Guillaume Bret and
Didier Rognan},
title = {Docking pose selection by interaction pattern graph similarity: application
to the {D3R} grand challenge 2015},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {669--683},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9930-3},
doi = {10.1007/S10822-016-9930-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SlynkoSBR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SouzaDNFS16,
author = {Raoni Almeida de Souza and
Natalia D{\'{\i}}az and
Ronaldo Alves Pinto Nagem and
Rafaela Salgado Ferreira and
Dimas Su{\'{a}}rez},
title = {Unraveling the distinctive features of hemorrhagic and non-hemorrhagic
snake venom metalloproteinases using molecular simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {1},
pages = {69--83},
year = {2016},
url = {https://doi.org/10.1007/s10822-015-9889-5},
doi = {10.1007/S10822-015-9889-5},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SouzaDNFS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SunseriRCK16,
author = {Jocelyn Sunseri and
Matthew Ragoza and
Jasmine Collins and
David Ryan Koes},
title = {A {D3R} prospective evaluation of machine learning for protein-ligand
scoring},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {761--771},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9960-x},
doi = {10.1007/S10822-016-9960-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SunseriRCK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TakedaWB16,
author = {Takako Takeda and
Yanli Wang and
Stephen H. Bryant},
title = {Structural insights of a PI3K/mTOR dual inhibitor with the morpholino-triazine
scaffold},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {4},
pages = {323--330},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9905-4},
doi = {10.1007/S10822-016-9905-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TakedaWB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ThaiTVNLHCL16,
author = {Nguyen Quoc Thai and
Ning{-}Hsuan Tseng and
Mui Thi Vu and
Tin Trung Nguyen and
Huynh Quang Linh and
Chin{-}Kun Hu and
Yun{-}Ru Chen and
Mai Suan Li},
title = {Discovery of {DNA} dyes Hoechst 34580 and 33342 as good candidates
for inhibiting amyloid beta formation: in silico and in vitro study},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {8},
pages = {639--650},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9932-1},
doi = {10.1007/S10822-016-9932-1},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ThaiTVNLHCL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ThangsunanKMKPH16,
author = {Patcharapong Thangsunan and
Sila Kittiwachana and
Puttinan Meepowpan and
Nawee Kungwan and
Panchika Prangkio and
Supa Hannongbua and
Nuttee Suree},
title = {Rapid activity prediction of {HIV-1} integrase inhibitors: harnessing
docking energetic components for empirical scoring by chemometric
and artificial neural network approaches},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {6},
pages = {471--488},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9917-0},
doi = {10.1007/S10822-016-9917-0},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ThangsunanKMKPH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TielkerTHKEGSK16,
author = {Nicolas Tielker and
Daniel Tomazic and
Jochen Heil and
Thomas Kloss and
Sebastian Ehrhart and
Stefan G{\"{u}}ssregen and
K. Friedemann Schmidt and
Stefan M. Kast},
title = {The {SAMPL5} challenge for embedded-cluster integral equation theory:
solvation free energies, aqueous p\emph{K} \({}_{\mbox{a}}\), and
cyclohexane-water log \emph{D}},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {11},
pages = {1035--1044},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9939-7},
doi = {10.1007/S10822-016-9939-7},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TielkerTHKEGSK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VogtSMB16,
author = {Martin Vogt and
Dagmar Stumpfe and
Gerald M. Maggiora and
J{\"{u}}rgen Bajorath},
title = {Lessons learned from the design of chemical space networks and opportunities
for new applications},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {3},
pages = {191--208},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9906-3},
doi = {10.1007/S10822-016-9906-3},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VogtSMB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Warr16,
author = {Wendy A. Warr},
title = {MOOCers and shakers and chemistry course takers},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {4},
pages = {281--284},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9908-1},
doi = {10.1007/S10822-016-9908-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Warr16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Warr16a,
author = {Wendy A. Warr},
title = {Blowing a breath of fresh share on data},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {12},
pages = {1143--1147},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9995-z},
doi = {10.1007/S10822-016-9995-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Warr16a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WilkesSB16,
author = {Jon G. Wilkes and
Iva B. Stoyanova{-}Slavova and
Dan A. Buzatu},
title = {Alignment-independent technique for 3D {QSAR} analysis},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {4},
pages = {331--345},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9909-0},
doi = {10.1007/S10822-016-9909-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WilkesSB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WuVMB16,
author = {Mengjun Wu and
Martin Vogt and
Gerald M. Maggiora and
J{\"{u}}rgen Bajorath},
title = {Design of chemical space networks on the basis of Tversky similarity},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {1},
pages = {1--12},
year = {2016},
url = {https://doi.org/10.1007/s10822-015-9891-y},
doi = {10.1007/S10822-015-9891-Y},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WuVMB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YanW16,
author = {Zhiqiang Yan and
Jin Wang},
title = {Incorporating specificity into optimization: evaluation of {SPA} using
{CSAR} 2014 and {CASF} 2013 benchmarks},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {3},
pages = {219--227},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9897-0},
doi = {10.1007/S10822-016-9897-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YanW16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YaoDCZWWWLC16,
author = {Zhi{-}Jiang Yao and
Jie Dong and
Yu{-}Jing Che and
Min{-}Feng Zhu and
Ming Wen and
Ning{-}Ning Wang and
Shan Wang and
Aiping Lu and
Dong{-}Sheng Cao},
title = {TargetNet: a web service for predicting potential drug-target interaction
profiling via multi-target {SAR} models},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {5},
pages = {413--424},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9915-2},
doi = {10.1007/S10822-016-9915-2},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YaoDCZWWWLC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YeBWC16,
author = {Zhaofeng Ye and
Matthew P. Baumgartner and
Bentley M. Wingert and
Carlos J. Camacho},
title = {Optimal strategies for virtual screening of induced-fit and flexible
target in the 2015 {D3R} Grand Challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {9},
pages = {695--706},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9941-0},
doi = {10.1007/S10822-016-9941-0},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YeBWC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhangDZHHKZ16,
author = {Hui Zhang and
Lan Ding and
Yi Zou and
Shui{-}Qing Hu and
Hai{-}Guo Huang and
Wei{-}Bao Kong and
Ji Zhang},
title = {Predicting drug-induced liver injury in human with Na{\"{\i}}ve
Bayes classifier approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {30},
number = {10},
pages = {889--898},
year = {2016},
url = {https://doi.org/10.1007/s10822-016-9972-6},
doi = {10.1007/S10822-016-9972-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZhangDZHHKZ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Abi-GhanemSP15,
author = {Jos{\'{e}}phine Abi{-}Ghanem and
Sergey A. Samsonov and
M. Teresa Pisabarro},
title = {Insights into the preferential order of strand exchange in the Cre/loxP
recombinase system: impact of the {DNA} spacer flanking sequence and
flexibility},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {3},
pages = {271--282},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9825-0},
doi = {10.1007/S10822-014-9825-0},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Abi-GhanemSP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AlamiddineSCMLT15,
author = {Zakaria Alamiddine and
Balaji Selvam and
Jos{\'{e}} Pedro Cer{\'{o}}n{-}Carrasco and
Monique Math{\'{e}}{-}Allainmat and
Jacques Lebreton and
Steeve H. Thany and
Ad{\`{e}}le D. Laurent and
J{\'{e}}r{\^{o}}me Graton and
Jean{-}Yves Le Questel},
title = {Molecular recognition of thiaclopride by Aplysia californica AChBP:
new insights from a computational investigation},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {12},
pages = {1151--1167},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9884-x},
doi = {10.1007/S10822-015-9884-X},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AlamiddineSCMLT15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AlbadaGW15,
author = {H. Bauke Albada and
Eyal Golub and
Itamar Willner},
title = {Computational docking simulations of a DNA-aptamer for argininamide
and related ligands},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {7},
pages = {643--654},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9844-5},
doi = {10.1007/S10822-015-9844-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AlbadaGW15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AliagasGHLOZK15,
author = {Ignacio Aliagas and
Alberto Gobbi and
Timothy Heffron and
Man{-}Ling Lee and
Daniel F. Ortwine and
Mark Zak and
S. Cyrus Khojasteh},
title = {A probabilistic method to report predictions from a human liver microsomes
stability {QSAR} model: a practical tool for drug discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {4},
pages = {327--338},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9838-3},
doi = {10.1007/S10822-015-9838-3},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AliagasGHLOZK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AnderssonHLQABE15,
author = {C. David Andersson and
J. Mikael Hillgren and
Cecilia M. Lindgren and
Weixing Qian and
Christine Akfur and
Lotta Berg and
Fredrik Ekstr{\"{o}}m and
Anna Linusson},
title = {Benefits of statistical molecular design, covariance analysis, and
reference models in {QSAR:} a case study on acetylcholinesterase},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {3},
pages = {199--215},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9808-1},
doi = {10.1007/S10822-014-9808-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AnderssonHLQABE15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BeckSK15,
author = {Bernd Beck and
Daniel Seeliger and
Jan M. Kriegl},
title = {The impact of data integrity on decision making in early lead discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {9},
pages = {911--921},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9871-2},
doi = {10.1007/S10822-015-9871-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BeckSK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BradleyWDGDM15,
author = {Anthony R. Bradley and
Ian D. Wall and
Frank von Delft and
Darren V. S. Green and
Charlotte M. Deane and
Brian D. Marsden},
title = {{WONKA:} objective novel complex analysis for ensembles of protein-ligand
structures},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {10},
pages = {963--973},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9866-z},
doi = {10.1007/S10822-015-9866-Z},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BradleyWDGDM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CappelDSD15,
author = {Daniel Cappel and
Steven L. Dixon and
Woody Sherman and
Jianxin Duan},
title = {Exploring conformational search protocols for ligand-based virtual
screening and 3-D {QSAR} modeling},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {2},
pages = {165--182},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9813-4},
doi = {10.1007/S10822-014-9813-4},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/CappelDSD15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Celis-BarrosSSCZ15,
author = {Cristian Celis{-}Barros and
Leslie Saavedra{-}Rivas and
J. Cristian Salgado and
Bruce K. Cassels and
Gerald Zapata{-}Torres},
title = {Molecular dynamics simulation of halogen bonding mimics experimental
data for cathepsin {L} inhibition},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {1},
pages = {37--46},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9802-7},
doi = {10.1007/S10822-014-9802-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Celis-BarrosSSCZ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChaudhariHL15,
author = {Rajan Chaudhari and
Andrew J. Heim and
Zhijun Li},
title = {Improving homology modeling of G-protein coupled receptors through
multiple-template derived conserved inter-residue interactions},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {5},
pages = {413--420},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9823-2},
doi = {10.1007/S10822-014-9823-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChaudhariHL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ClevesJ15,
author = {Ann E. Cleves and
Ajay N. Jain},
title = {Chemical and protein structural basis for biological crosstalk between
PPAR{\(\alpha\)} and {COX} enzymes},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {2},
pages = {101--112},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9815-2},
doi = {10.1007/S10822-014-9815-2},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ClevesJ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ClevesJ15a,
author = {Ann E. Cleves and
Ajay N. Jain},
title = {Knowledge-guided docking: accurate prospective prediction of bound
configurations of novel ligands using Surflex-Dock},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {6},
pages = {485--509},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9846-3},
doi = {10.1007/S10822-015-9846-3},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ClevesJ15a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ColcloughW15,
author = {Nicola Colclough and
Mark C. Wenlock},
title = {Interpreting physicochemical experimental data sets},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {9},
pages = {779--794},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9850-7},
doi = {10.1007/S10822-015-9850-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ColcloughW15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Della-LongaA15,
author = {Stefano Della{-}Longa and
Alessandro Arcovito},
title = {Intermediate states in the binding process of folic acid to folate
receptor {\(\alpha\)}: insights by molecular dynamics and metadynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {1},
pages = {23--35},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9801-8},
doi = {10.1007/S10822-014-9801-8},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Della-LongaA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DellerR15,
author = {Marc C. Deller and
Bernhard Rupp},
title = {Models of protein-ligand crystal structures: trust, but verify},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {9},
pages = {817--836},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9833-8},
doi = {10.1007/S10822-015-9833-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DellerR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DhokeLDASB15,
author = {Gaurao V. Dhoke and
Christoph Loderer and
Mehdi D. Davari and
Marion Ansorge{-}Schumacher and
Ulrich Schwaneberg and
Marco Bocola},
title = {Activity prediction of substrates in NADH-dependent carbonyl reductase
by docking requires catalytic constraints and charge parameterization
of catalytic zinc environment},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {11},
pages = {1057--1069},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9878-8},
doi = {10.1007/S10822-015-9878-8},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/DhokeLDASB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DiazLEH15,
author = {Carlos Diaz and
Ligia Llovera and
Lorenzo Echevarria and
Florencio E. Hern{\'{a}}ndez},
title = {Assessment of the tautomeric population of benzimidazole derivatives
in solution: a simple and versatile theoretical-experimental approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {2},
pages = {143--154},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9810-7},
doi = {10.1007/S10822-014-9810-7},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DiazLEH15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DillerCW15,
author = {David J. Diller and
Nancy D. Connell and
William J. Welsh},
title = {Avalanche for shape and feature-based virtual screening with 3D alignment},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {11},
pages = {1015--1024},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9875-y},
doi = {10.1007/S10822-015-9875-Y},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/DillerCW15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Durmaz15,
author = {Vedat Durmaz},
title = {Markov model-based polymer assembly from force field-parameterized
building blocks},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {3},
pages = {225--232},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9817-0},
doi = {10.1007/S10822-014-9817-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Durmaz15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FengABBBKLOTWG15,
author = {Jianwen A. Feng and
Ignacio Aliagas and
Philippe Bergeron and
Jeffrey M. Blaney and
Erin K. Bradley and
Michael F. T. Koehler and
Man{-}Ling Lee and
Daniel F. Ortwine and
Vickie Tsui and
Johnny Wu and
Alberto Gobbi},
title = {An integrated suite of modeling tools that empower scientists in structure-
and property-based drug design},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {6},
pages = {511--523},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9845-4},
doi = {10.1007/S10822-015-9845-4},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FengABBBKLOTWG15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FengZDFH15,
author = {Tingting Feng and
Yanjun Zhang and
Jing{-}Na Ding and
Song Fan and
Ju{-}Guang Han},
title = {Insights into resistance mechanism of the macrolide biosensor protein
MphR(A) binding to macrolide antibiotic erythromycin by molecular
dynamics simulation},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {12},
pages = {1123--1136},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9881-0},
doi = {10.1007/S10822-015-9881-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FengZDFH15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FernandezOMPF15,
author = {David Fern{\'{a}}ndez and
Joaqu{\'{\i}}n Ortega{-}Castro and
Laura Mari{\~{n}}o and
Joan Perell{\'{o}} and
Juan Frau},
title = {Mechanistic insights into protonation state as a critical factor in
hFPPS enzyme inhibition},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {7},
pages = {667--680},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9853-4},
doi = {10.1007/S10822-015-9853-4},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/FernandezOMPF15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GallicchioCCFGH15,
author = {Emilio Gallicchio and
Haoyuan Chen and
He Chen and
Michael Fitzgerald and
Yang Gao and
Peng He and
Malathi Kalyanikar and
Chuan Kao and
Beidi Lu and
Yijie Niu and
Manasi A. Pethe and
Jie Zhu and
Ronald M. Levy},
title = {{BEDAM} binding free energy predictions for the {SAMPL4} octa-acid
host challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {4},
pages = {315--325},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9795-2},
doi = {10.1007/S10822-014-9795-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GallicchioCCFGH15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GarnettGVB15,
author = {Roman Garnett and
Thomas G{\"{a}}rtner and
Martin Vogt and
J{\"{u}}rgen Bajorath},
title = {Introducing the 'active search' method for iterative virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {4},
pages = {305--314},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9832-9},
doi = {10.1007/S10822-015-9832-9},
timestamp = {Mon, 30 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GarnettGVB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GiantiZ15,
author = {Eleonora Gianti and
Randy J. Zauhar},
title = {An {SH2} domain model of {STAT5} in complex with phospho-peptides
define "STAT5 Binding Signatures"},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {5},
pages = {451--470},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9835-6},
doi = {10.1007/S10822-015-9835-6},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GiantiZ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Guthrie15,
author = {J. Peter Guthrie},
title = {Presenting data in such a fashion that they can be used by other scientists},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {9},
pages = {837--846},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9868-x},
doi = {10.1007/S10822-015-9868-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Guthrie15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HansonEC15,
author = {Sonya M. Hanson and
Sean Ekins and
John D. Chodera},
title = {Modeling error in experimental assays using the bootstrap principle:
understanding discrepancies between assays using different dispensing
technologies},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {12},
pages = {1073--1086},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9888-6},
doi = {10.1007/S10822-015-9888-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HansonEC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JaradatKHT15,
author = {Nour Jamal Jaradat and
Mohammad A. Khanfar and
Maha Habash and
Mutasem Omar Taha},
title = {Combining docking-based comparative intermolecular contacts analysis
and k-nearest neighbor correlation for the discovery of new check
point kinase 1 inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {6},
pages = {561--581},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9848-1},
doi = {10.1007/S10822-015-9848-1},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JaradatKHT15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Jones15,
author = {Gareth Jones},
title = {Fitting and handling dose response data},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {1},
pages = {1--11},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9752-0},
doi = {10.1007/S10822-014-9752-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Jones15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KalinowskaFSR15,
author = {Barbara Kalinowska and
Piotr Fabian and
Katarzyna Stapor and
Irena Roterman},
title = {Statistical dictionaries for hypothetical in silico model of the early-stage
intermediate in protein folding},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {7},
pages = {609--618},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9839-2},
doi = {10.1007/S10822-015-9839-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KalinowskaFSR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KangP15,
author = {Hyun{-}Jin Kang and
Hyun{-}Ju Park},
title = {In silico identification of novel ligands for G-quadruplex in the
c-MYC promoter},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {4},
pages = {339--348},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9826-z},
doi = {10.1007/S10822-014-9826-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KangP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KelemenFK15,
author = {{\'{A}}d{\'{a}}m A. Kelemen and
Gy{\"{o}}rgy G. Ferenczy and
Gy{\"{o}}rgy M. Keser{\"{u}}},
title = {A desirability function-based scoring scheme for selecting fragment-like
class {A} aminergic {GPCR} ligands},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {1},
pages = {59--66},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9804-5},
doi = {10.1007/S10822-014-9804-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KelemenFK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KelemenFK15a,
author = {{\'{A}}d{\'{a}}m A. Kelemen and
Gy{\"{o}}rgy G. Ferenczy and
Gy{\"{o}}rgy M. Keser{\"{u}}},
title = {Erratum to: {A} desirability function-based scoring scheme for selecting
fragment-like class {A} aminergic {GPCR} ligands},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {1},
pages = {67},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9812-5},
doi = {10.1007/S10822-014-9812-5},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KelemenFK15a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KlimovichM15,
author = {Pavel V. Klimovich and
David L. Mobley},
title = {A Python tool to set up relative free energy calculations in {GROMACS}},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {11},
pages = {1007--1014},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9873-0},
doi = {10.1007/S10822-015-9873-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KlimovichM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KlimovichSM15,
author = {Pavel V. Klimovich and
Michael R. Shirts and
David L. Mobley},
title = {Guidelines for the analysis of free energy calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {5},
pages = {397--411},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9840-9},
doi = {10.1007/S10822-015-9840-9},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KlimovichSM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KoppisettyFLN15,
author = {Chaitanya A. K. Koppisetty and
Martin Frank and
Alexander Lyubartsev and
Per{-}Georg Nyholm},
title = {Binding energy calculations for hevein-carbohydrate interactions using
expanded ensemble molecular dynamics simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {1},
pages = {13--21},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9792-5},
doi = {10.1007/S10822-014-9792-5},
timestamp = {Thu, 16 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KoppisettyFLN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KramerCS15,
author = {Christian Kramer and
John D. Chodera and
Terry R. Stouch},
title = {Introduction to the special issue: Data Part 2: Experimental Data},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {9},
pages = {777},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9874-z},
doi = {10.1007/S10822-015-9874-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KramerCS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KrimmerK15,
author = {Stefan G. Krimmer and
Gerhard Klebe},
title = {Thermodynamics of protein-ligand interactions as a reference for computational
analysis: how to assess accuracy, reliability and relevance of experimental
data},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {9},
pages = {867--883},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9867-y},
doi = {10.1007/S10822-015-9867-Y},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KrimmerK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LeonKDSB15,
author = {Antonio de la Vega de Le{\'{o}}n and
Shilva Kayastha and
Dilyana Dimova and
Thomas Schultz and
J{\"{u}}rgen Bajorath},
title = {Visualization of multi-property landscapes for compound selection
and optimization},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {8},
pages = {695--705},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9862-3},
doi = {10.1007/S10822-015-9862-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LeonKDSB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LewisGHBB15,
author = {Stephanie N. Lewis and
Zulma Garcia and
Raquel Hontecillas and
Josep Bassaganya{-}Riera and
David R. Bevan},
title = {Pharmacophore modeling improves virtual screening for novel peroxisome
proliferator-activated receptor-gamma ligands},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {5},
pages = {421--439},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9831-x},
doi = {10.1007/S10822-015-9831-X},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LewisGHBB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiDBPCLHZB15,
author = {Yan Li and
Michel Delamar and
Patricia Busca and
Guillaume Prestat and
Laurent Le Corre and
Laurence Legeai{-}Mallet and
Rongjing Hu and
Ruisheng Zhang and
Florent Barbault},
title = {Molecular modeling study of the induced-fit effect on kinase inhibition:
the case of fibroblast growth factor receptor 3 {(FGFR3)}},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {7},
pages = {619--641},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9841-8},
doi = {10.1007/S10822-015-9841-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiDBPCLHZB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiLD15,
author = {Yan Li and
Xiang Li and
Zigang Dong},
title = {Statistical analysis of {EGFR} structures' performance in virtual
screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {11},
pages = {1045--1055},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9877-9},
doi = {10.1007/S10822-015-9877-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiLD15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LindertTNBM15,
author = {Steffen Lindert and
Lorillee Tallorin and
Quynh G. Nguyen and
Michael D. Burkart and
James Andrew McCammon},
title = {In silico screening for Plasmodium falciparum enoyl-ACP reductase
inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {1},
pages = {79--87},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9806-3},
doi = {10.1007/S10822-014-9806-3},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LindertTNBM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MartinC15,
author = {Eric Martin and
Eddie Cao},
title = {Euclidean chemical spaces from molecular fingerprints: Hamming distance
and Hempel's ravens},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {5},
pages = {387--395},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9819-y},
doi = {10.1007/S10822-014-9819-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MartinC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/McGannNE15,
author = {Mark McGann and
Anthony Nicholls and
Istvan J. Enyedy},
title = {The statistics of virtual screening and lead optimization},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {10},
pages = {923--936},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9861-4},
doi = {10.1007/S10822-015-9861-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/McGannNE15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MondalCCB15,
author = {Manas Mondal and
Devapriya Choudhury and
Jaydeb Chakrabarti and
Dhananjay Bhattacharyya},
title = {Role of indirect readout mechanism in {TATA} box binding protein-DNA
interaction},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {3},
pages = {283--295},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9828-x},
doi = {10.1007/S10822-014-9828-X},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MondalCCB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MunizN15,
author = {Heloisa dos Santos Muniz and
Alessandro S. Nascimento},
title = {Ligand- and receptor-based docking with LiBELa},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {8},
pages = {713--723},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9856-1},
doi = {10.1007/S10822-015-9856-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MunizN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NabuNOLILWP15,
author = {Sunanta Nabu and
Chanin Nantasenamat and
Wiwat Owasirikul and
Ratana Lawung and
Chartchalerm Isarankura{-}Na{-}Ayudhya and
Maris Lapins and
Jarl E. S. Wikberg and
Virapong Prachayasittikul},
title = {Proteochemometric model for predicting the inhibition of penicillin-binding
proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {2},
pages = {127--141},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9809-0},
doi = {10.1007/S10822-014-9809-0},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/NabuNOLILWP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NiinivehmasSLRP15,
author = {Sanna P. Niinivehmas and
Kari Salokas and
Sakari L{\"{a}}tti and
Hannu Raunio and
Olli T. Pentik{\"{a}}inen},
title = {Ultrafast protein structure-based virtual screening with Panther},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {10},
pages = {989--1006},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9870-3},
doi = {10.1007/S10822-015-9870-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NiinivehmasSLRP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NikolicMBMSCRMARM15,
author = {Katarina Nikolic and
Lazaros Mavridis and
Oscar M. Bautista{-}Aguilera and
Jos{\'{e}} Marco{-}Contelles and
Holger Stark and
Maria do Carmo Carreiras and
Ilaria Rossi and
Paola Massarelli and
Danica Agbaba and
Rona R. Ramsay and
John B. O. Mitchell},
title = {Predicting targets of compounds against neurological diseases using
cheminformatic methodology},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {2},
pages = {183--198},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9816-1},
doi = {10.1007/S10822-014-9816-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NikolicMBMSCRMARM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OgrizekTLSHMKJG15,
author = {Mitja Ogrizek and
Samo Turk and
Samo Lesnik and
Izidor Sosic and
Milan Hodoscek and
Bojana Mirkovic and
Janko Kos and
Dusanka Janezic and
Stanislav Gobec and
Janez Konc},
title = {Molecular dynamics to enhance structure-based virtual screening on
cathepsin {B}},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {8},
pages = {707--712},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9847-2},
doi = {10.1007/S10822-015-9847-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OgrizekTLSHMKJG15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PangYCSCLYZZAH15,
author = {Chunli Pang and
Hong{-}Bo Yuan and
Tianguang Cao and
Ji{-}Guo Su and
Ya{-}Fei Chen and
Hui Liu and
Hui Yu and
Hai{-}Ling Zhang and
Yong Zhan and
Hailong An and
Yue{-}Bin Han},
title = {Molecular simulation assisted identification of Ca2+ binding residues
in {TMEM16A}},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {11},
pages = {1035--1043},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9876-x},
doi = {10.1007/S10822-015-9876-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PangYCSCLYZZAH15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PaolettaSKHKHAS15,
author = {Silvia Paoletta and
Davide Sabbadin and
Ivar von K{\"{u}}gelgen and
Sonja Hinz and
Vsevolod Katritch and
Kristina Hoffmann and
Aliaa Abdelrahman and
Jens Stra{\ss}burger and
Younis Baqi and
Qiang Zhao and
Raymond C. Stevens and
Stefano Moro and
Christa E. M{\"{u}}ller and
Kenneth A. Jacobson},
title = {Modeling ligand recognition at the {P2Y12} receptor in light of X-ray
structural information},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {8},
pages = {737--756},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9858-z},
doi = {10.1007/S10822-015-9858-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PaolettaSKHKHAS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PapadatosGHO15,
author = {George Papadatos and
Anna Gaulton and
Anne Hersey and
John P. Overington},
title = {Activity, assay and target data curation and quality in the ChEMBL
database},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {9},
pages = {885--896},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9860-5},
doi = {10.1007/S10822-015-9860-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PapadatosGHO15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PatilPGRGBNTS15,
author = {Sachin P. Patil and
Michael F. Pacitti and
Kevin S. Gilroy and
John C. Ruggiero and
Jonathan D. Griffin and
Joseph J. Butera and
Joseph M. Notarfrancesco and
Shawn Tran and
John W. Stoddart},
title = {Identification of antipsychotic drug fluspirilene as a potential p53-MDM2
inhibitor: a combined computational and experimental study},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {2},
pages = {155--163},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9811-6},
doi = {10.1007/S10822-014-9811-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PatilPGRGBNTS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PerdihHPBGKGSW15,
author = {Andrej Perdih and
Martina Hrast and
Kaja Pureber and
H{\'{e}}l{\`{e}}ne Barreteau and
Simona Golic Grdadolnik and
Darko Kocjan and
Stanislav Gobec and
Tomaz Solmajer and
Gerhard Wolber},
title = {Furan-based benzene mono- and dicarboxylic acid derivatives as multiple
inhibitors of the bacterial Mur ligases (MurC-MurF): experimental
and computational characterization},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {6},
pages = {541--560},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9843-6},
doi = {10.1007/S10822-015-9843-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PerdihHPBGKGSW15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PihanDTPLBD15,
author = {Emilie Pihan and
Roberto F. Delgadillo and
Michelle L. Tonkin and
Martine Pugni{\`{e}}re and
Maryse Lebrun and
Martin J. Boulanger and
Dominique Douguet},
title = {Computational and biophysical approaches to protein-protein interaction
inhibition of Plasmodium falciparum {AMA1/RON2} complex},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {6},
pages = {525--539},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9842-7},
doi = {10.1007/S10822-015-9842-7},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PihanDTPLBD15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RagnoBPWPHPK15,
author = {Rino Ragno and
Flavio Ballante and
Adele Pirolli and
Richard B. Wickersham III and
Alexandros Patsilinakos and
St{\'{e}}phanie Hesse and
Enrico Perspicace and
Gilbert Kirsch},
title = {Vascular endothelial growth factor receptor-2 {(VEGFR-2)} inhibitors:
development and validation of predictive 3-D {QSAR} models through
extensive ligand- and structure-based approaches},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {8},
pages = {757--776},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9859-y},
doi = {10.1007/S10822-015-9859-Y},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RagnoBPWPHPK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RoosHOPHGEN15,
author = {Katarina Roos and
Anders Hogner and
Derek Ogg and
Martin J. Packer and
Eva Hansson and
Kenneth L. Granberg and
Emma Evertsson and
Anneli Nordqvist},
title = {Predicting the relative binding affinity of mineralocorticoid receptor
antagonists by density functional methods},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {12},
pages = {1109--1122},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9880-1},
doi = {10.1007/S10822-015-9880-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/RoosHOPHGEN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SaezV15,
author = {David Adrian Saez and
Esteban V{\"{o}}hringer{-}Martinez},
title = {A consistent S-Adenosylmethionine force field improved by dynamic
Hirshfeld-I atomic charges for biomolecular simulation},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {10},
pages = {951--961},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9864-1},
doi = {10.1007/S10822-015-9864-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SaezV15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Sahlin15,
author = {Ullrika Sahlin},
title = {Assessment of uncertainty in chemical models by Bayesian probabilities:
Why, when, how?},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {7},
pages = {583--594},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9822-3},
doi = {10.1007/S10822-014-9822-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Sahlin15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SangeethaMA15,
author = {Balasubramanian Sangeetha and
Muthukumaran Rajagopalan and
Amutha Ramaswamy},
title = {Structural dynamics of native and {V260E} mutant C-terminal domain
of {HIV-1} integrase},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {4},
pages = {371--385},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9830-y},
doi = {10.1007/S10822-015-9830-Y},
timestamp = {Tue, 26 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SangeethaMA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SantoshiMSSSJLK15,
author = {Seneha Santoshi and
Naresh Kumar Manchukonda and
Charu Suri and
Manya Sharma and
Balasubramanian Sridhar and
Silja Joseph and
Manu Lopus and
Srinivas Kantevari and
Iswar Baitharu and
Pradeep Kumar Naik},
title = {Rational design of biaryl pharmacophore inserted noscapine derivatives
as potent tubulin binding anticancer agents},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {3},
pages = {249--270},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9820-5},
doi = {10.1007/S10822-014-9820-5},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SantoshiMSSSJLK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SarvagallaSKSLHHC15,
author = {Sailu Sarvagalla and
Vivek Kumar Singh and
Yi{-}Yu Ke and
Hui{-}Yi Shiao and
Wen{-}Hsing Lin and
Hsing{-}Pang Hsieh and
John T. A. Hsu and
Mohane Selvaraj Coumar},
title = {Identification of ligand efficient, fragment-like hits from an {HTS}
library: structure-based virtual screening and docking investigations
of 2H- and 3H-pyrazolo tautomers for Aurora kinase {A} selectivity},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {1},
pages = {89--100},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9807-2},
doi = {10.1007/S10822-014-9807-2},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SarvagallaSKSLHHC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SchallerCDOHM15,
author = {Andrea Schaller and
Natalie K. Connors and
Mirjana Dimitrijev Dwyer and
Stefan A. Oelmeier and
J{\"{u}}rgen Hubbuch and
Anton P. J. Middelberg},
title = {Computational study of elements of stability of a four-helix bundle
protein biosurfactant},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {1},
pages = {47--58},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9803-6},
doi = {10.1007/S10822-014-9803-6},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SchallerCDOHM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SegallC15,
author = {Matthew D. Segall and
Edmund J. Champness},
title = {The challenges of making decisions using uncertain data},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {9},
pages = {809--816},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9855-2},
doi = {10.1007/S10822-015-9855-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SegallC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SgrignaniNCG15,
author = {Jacopo Sgrignani and
Beatrice Novati and
Giorgio Colombo and
Giovanni Grazioso},
title = {Covalent docking of selected boron-based serine beta-lactamase inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {5},
pages = {441--450},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9834-7},
doi = {10.1007/S10822-015-9834-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SgrignaniNCG15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SidorovGMVH15,
author = {Pavel Sidorov and
H{\'{e}}l{\'{e}}na A. Gaspar and
Gilles Marcou and
Alexandre Varnek and
Dragos Horvath},
title = {Mappability of drug-like space: towards a polypharmacologically competent
map of drug-relevant compounds},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {12},
pages = {1087--1108},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9882-z},
doi = {10.1007/S10822-015-9882-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SidorovGMVH15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SitnikovZUVB15,
author = {Gleb V. Sitnikov and
Nelly I. Zhokhova and
Yury A. Ustynyuk and
Alexandre Varnek and
Igor I. Baskin},
title = {Continuous indicator fields: a novel universal type of molecular fields},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {3},
pages = {233--247},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9818-z},
doi = {10.1007/S10822-014-9818-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SitnikovZUVB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SmithR15,
author = {Jennifer M. Smith and
Christopher N. Rowley},
title = {Automated computational screening of the thiol reactivity of substituted
alkenes},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {8},
pages = {725--735},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9857-0},
doi = {10.1007/S10822-015-9857-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SmithR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TsujiSK15,
author = {Motonori Tsuji and
Koichi Shudo and
Hiroyuki Kagechika},
title = {Docking simulations suggest that all-trans retinoic acid could bind
to retinoid {X} receptors},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {10},
pages = {975--988},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9869-9},
doi = {10.1007/S10822-015-9869-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TsujiSK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/UnanYT15,
author = {Hulya Unan and
Ahmet Yildirim and
Mustafa Tekpinar},
title = {Opening mechanism of adenylate kinase can vary according to selected
molecular dynamics force field},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {7},
pages = {655--665},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9849-0},
doi = {10.1007/S10822-015-9849-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/UnanYT15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VassJBPKT15,
author = {M{\'{a}}rton Vass and
Bal{\'{a}}zs J{\'{o}}j{\'{a}}rt and
Ferenc Bog{\'{a}}r and
G{\'{a}}bor Paragi and
Gy{\"{o}}rgy M. Keser{\"{u}} and
{\'{A}}kos Tarcsay},
title = {Dynamics and structural determinants of ligand recognition of the
5-HT6 receptor},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {12},
pages = {1137--1149},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9883-y},
doi = {10.1007/S10822-015-9883-Y},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VassJBPKT15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ViscontiECE15,
author = {Alessia Visconti and
Giuseppe Ermondi and
Giulia Caron and
Roberto Esposito},
title = {Prediction and interpretation of the lipophilicity of small peptides},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {4},
pages = {361--370},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9829-4},
doi = {10.1007/S10822-015-9829-4},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ViscontiECE15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WaldmanFC15,
author = {Marvin Waldman and
Robert Fraczkiewicz and
Robert D. Clark},
title = {Tales from the war on error: the art and science of curating {QSAR}
data},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {9},
pages = {897--910},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9865-0},
doi = {10.1007/S10822-015-9865-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WaldmanFC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WangC15,
author = {Yeng{-}Tseng Wang and
Lea{-}Yea Chuang},
title = {Insight into the modified Ibalizumab-human {CD4} receptor interactions:
using a computational binding free energy approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {1},
pages = {69--78},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9805-4},
doi = {10.1007/S10822-014-9805-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WangC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WangGKPJZL15,
author = {Yu Wang and
Yanzhi Guo and
Qifan Kuang and
Xuemei Pu and
Yue Ji and
Zhihang Zhang and
Menglong Li},
title = {A comparative study of family-specific protein-ligand complex affinity
prediction based on random forest approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {4},
pages = {349--360},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9827-y},
doi = {10.1007/S10822-014-9827-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WangGKPJZL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Warr15,
author = {Wendy A. Warr},
title = {App-etite for change},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {4},
pages = {297--303},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9824-1},
doi = {10.1007/S10822-014-9824-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Warr15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Warr15a,
author = {Wendy A. Warr},
title = {Many InChIs and quite some feat},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {8},
pages = {681--694},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9854-3},
doi = {10.1007/S10822-015-9854-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Warr15a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WatzigOSANEABEB15,
author = {Hermann W{\"{a}}tzig and
Imke Oltmann{-}Norden and
Franziska Steinicke and
Hassan A. Alhazmi and
Markus Nachbar and
Deia Abd El{-}Hady and
Hassan M. Albishri and
Knut Baumann and
Thomas E. Exner and
Frank M. Boeckler and
Sami El Deeb},
title = {Data quality in drug discovery: the role of analytical performance
in ligand binding assays},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {9},
pages = {847--865},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9851-6},
doi = {10.1007/S10822-015-9851-6},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/WatzigOSANEABEB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WiniwarterMJCLP15,
author = {Susanne Winiwarter and
Brian Middleton and
Barry Jones and
Paul Courtney and
Bo Lindmark and
Ken M. Page and
Alan Clark and
Claire Landqvist},
title = {Time dependent analysis of assay comparability: a novel approach to
understand intra- and inter-site variability over time},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {9},
pages = {795--807},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9836-5},
doi = {10.1007/S10822-015-9836-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WiniwarterMJCLP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Wolf15,
author = {Romain M. Wolf},
title = {Extracting ligands from receptors by reversed targeted molecular dynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {11},
pages = {1025--1034},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9863-2},
doi = {10.1007/S10822-015-9863-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Wolf15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZanithP15,
author = {Caroline C. Zanith and
Josefredo R. Pliego Jr.},
title = {Performance of the {SMD} and {SM8} models for predicting solvation
free energy of neutral solutes in methanol, dimethyl sulfoxide and
acetonitrile},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {3},
pages = {217--224},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9814-3},
doi = {10.1007/S10822-014-9814-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZanithP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhangG15,
author = {Xueli Zhang and
Xuedong Gong},
title = {A simple, fast and convenient new method for predicting the stability
of nitro compounds},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {5},
pages = {471--483},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9837-4},
doi = {10.1007/S10822-015-9837-4},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZhangG15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhangVMB15,
author = {Bijun Zhang and
Martin Vogt and
Gerald M. Maggiora and
J{\"{u}}rgen Bajorath},
title = {Comparison of bioactive chemical space networks generated using substructure-
and fingerprint-based measures of molecular similarity},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {7},
pages = {595--608},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9852-5},
doi = {10.1007/S10822-015-9852-5},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZhangVMB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhangVMB15a,
author = {Bijun Zhang and
Martin Vogt and
Gerald M. Maggiora and
J{\"{u}}rgen Bajorath},
title = {Design of chemical space networks using a Tanimoto similarity variant
based upon maximum common substructures},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {10},
pages = {937--950},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9872-1},
doi = {10.1007/S10822-015-9872-1},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZhangVMB15a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhangVMB15b,
author = {Bijun Zhang and
Martin Vogt and
Gerald M. Maggiora and
J{\"{u}}rgen Bajorath},
title = {Erratum to: Design of chemical space networks using a Tanimoto similarity
variant based upon maximum common substructures},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {11},
pages = {1071--1072},
year = {2015},
url = {https://doi.org/10.1007/s10822-015-9879-7},
doi = {10.1007/S10822-015-9879-7},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZhangVMB15b.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZwierzynaVMB15,
author = {Magdalena Zwierzyna and
Martin Vogt and
Gerald M. Maggiora and
J{\"{u}}rgen Bajorath},
title = {Design and characterization of chemical space networks for different
compound data sets},
journal = {J. Comput. Aided Mol. Des.},
volume = {29},
number = {2},
pages = {113--125},
year = {2015},
url = {https://doi.org/10.1007/s10822-014-9821-4},
doi = {10.1007/S10822-014-9821-4},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZwierzynaVMB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Arenas-SalinasOGPHQ14,
author = {Mauricio Arenas{-}Salinas and
Samuel Ortega{-}Salazar and
Fernando Gonzales{-}Nilo and
Ehmke Pohl and
David S. Holmes and
Raquel Quatrini},
title = {{AFAL:} a web service for profiling amino acids surrounding ligands
in proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {11},
pages = {1069--1076},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9783-6},
doi = {10.1007/S10822-014-9783-6},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Arenas-SalinasOGPHQ14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BarrosoBAR14,
author = {Telma Barroso and
Ricardo J. F. Branco and
Ana Aguiar{-}Ricardo and
Ana C. A. Roque},
title = {Structural evaluation of an alternative Protein {A} biomimetic ligand
for antibody purification},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {1},
pages = {25--34},
year = {2014},
url = {https://doi.org/10.1007/s10822-013-9703-1},
doi = {10.1007/S10822-013-9703-1},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BarrosoBAR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BecksteinFI14,
author = {Oliver Beckstein and
Ana{\"{\i}}s Fourrier and
Bogdan I. Iorga},
title = {Prediction of hydration free energies for the {SAMPL4} diverse set
of compounds using molecular dynamics simulations with the {OPLS-AA}
force field},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {265--276},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9727-1},
doi = {10.1007/S10822-014-9727-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BecksteinFI14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BermanKNM14,
author = {Helen M. Berman and
Gerard J. Kleywegt and
Haruki Nakamura and
John L. Markley},
title = {The Protein Data Bank archive as an open data resource},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {10},
pages = {1009--1014},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9770-y},
doi = {10.1007/S10822-014-9770-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BermanKNM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BrownOMVH14,
author = {J. B. Brown and
Yasushi Okuno and
Gilles Marcou and
Alexandre Varnek and
Dragos Horvath},
title = {Computational chemogenomics: Is it more than inductive transfer?},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {6},
pages = {597--618},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9743-1},
doi = {10.1007/S10822-014-9743-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BrownOMVH14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BrunoG14,
author = {Ian J. Bruno and
Colin R. Groom},
title = {A crystallographic perspective on sharing data and knowledge},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {10},
pages = {1015--1022},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9780-9},
doi = {10.1007/S10822-014-9780-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BrunoG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ColasI14,
author = {Claire Colas and
Bogdan I. Iorga},
title = {Virtual screening of the {SAMPL4} blinded {HIV} integrase inhibitors
dataset},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {455--462},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9707-5},
doi = {10.1007/S10822-014-9707-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ColasI14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ColemanSW14,
author = {Ryan G. Coleman and
Teague Sterling and
Dahlia R. Weiss},
title = {{SAMPL4} {\&} {DOCK3.7:} lessons for automated docking procedures},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {201--209},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9722-6},
doi = {10.1007/S10822-014-9722-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ColemanSW14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ComitaniCABLM14,
author = {Federico Comitani and
Netta Cohen and
Jamie Ashby and
Dominic Botten and
Sarah C. R. Lummis and
Carla Molteni},
title = {Insights into the binding of {GABA} to the insect {RDL} receptor from
atomistic simulations: a comparison of models},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {1},
pages = {35--48},
year = {2014},
url = {https://doi.org/10.1007/s10822-013-9704-0},
doi = {10.1007/S10822-013-9704-0},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ComitaniCABLM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Czodrowski14,
author = {Paul Czodrowski},
title = {Count on kappa},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {11},
pages = {1049--1055},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9759-6},
doi = {10.1007/S10822-014-9759-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Czodrowski14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/EbinaSTK14,
author = {Teppei Ebina and
Ryosuke Suzuki and
Ryotaro Tsuji and
Yutaka Kuroda},
title = {{H-DROP:} an {SVM} based helical domain linker predictor trained with
features optimized by combining random forest and stepwise selection},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {8},
pages = {831--839},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9763-x},
doi = {10.1007/S10822-014-9763-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/EbinaSTK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/EidSZV14,
author = {Sameh Eid and
Noureldin Saleh and
Adam Zalewski and
Angelo Vedani},
title = {Exploring the free-energy landscape of carbohydrate-protein complexes:
development and validation of scoring functions considering the binding-site
topology},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {12},
pages = {1191--1204},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9794-3},
doi = {10.1007/S10822-014-9794-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/EidSZV14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/EkinsCSLW14,
author = {Sean Ekins and
Alex M. Clark and
S. Joshua Swamidass and
Nadia K. Litterman and
Antony J. Williams},
title = {Bigger data, collaborative tools and the future of predictive drug
discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {10},
pages = {997--1008},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9762-y},
doi = {10.1007/S10822-014-9762-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/EkinsCSLW14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/EllingsonGWBSN14,
author = {Benjamin A. Ellingson and
Matthew T. Geballe and
Stanislaw Wlodek and
Christopher I. Bayly and
A. Geoffrey Skillman and
Anthony Nicholls},
title = {Efficient calculation of {SAMPL4} hydration free energies using OMEGA,
SZYBKI, QUACPAC, and Zap {TK}},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {289--298},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9720-8},
doi = {10.1007/S10822-014-9720-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/EllingsonGWBSN14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FayazR14,
author = {S. M. Fayaz and
G. Krishnamurthy Rajanikant},
title = {Ensemble pharmacophore meets ensemble docking: a novel screening strategy
for the identification of {RIPK1} inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {7},
pages = {779--794},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9771-x},
doi = {10.1007/S10822-014-9771-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FayazR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ForceR14,
author = {Megan M. Force and
Nigel J. Robinson},
title = {Encouraging data citation and discovery with the Data Citation Index},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {10},
pages = {1043--1048},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9768-5},
doi = {10.1007/S10822-014-9768-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ForceR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Franco-GonzalezRCM14,
author = {Juan Felipe Franco{-}Gonzalez and
Javier Ramos and
Victor L. Cruz and
Javier Mart{\'{\i}}nez{-}Salazar},
title = {Exploring the dynamics and interaction of a full ErbB2 receptor and
Trastuzumab-Fab antibody in a lipid bilayer model using Martini coarse-grained
force field},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {11},
pages = {1093--1107},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9787-2},
doi = {10.1007/S10822-014-9787-2},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Franco-GonzalezRCM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FreyB14,
author = {Jeremy G. Frey and
Colin L. Bird},
title = {Scientific and technical data sharing: a trading perspective},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {10},
pages = {989--996},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9785-4},
doi = {10.1007/S10822-014-9785-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FreyB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FuLW14,
author = {Jia Fu and
Yu Liu and
Jianzhong Wu},
title = {Fast prediction of hydration free energies for {SAMPL4} blind test
from a classical density functional theory},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {299--304},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9730-6},
doi = {10.1007/S10822-014-9730-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FuLW14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GallicchioDHWPSFOL14,
author = {Emilio Gallicchio and
Nan{-}Jie Deng and
Peng He and
Lauren Wickstrom and
Alexander L. Perryman and
Daniel N. Santiago and
Stefano Forli and
Arthur J. Olson and
Ronald M. Levy},
title = {Virtual screening of integrase inhibitors by large scale binding free
energy calculations: the {SAMPL4} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {475--490},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9711-9},
doi = {10.1007/S10822-014-9711-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GallicchioDHWPSFOL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GeeWRSKY14,
author = {Veronica M. W. Gee and
Fiona S. L. Wong and
Lalitha Ramachandran and
Gautam Sethi and
Alan Prem Kumar and
Chun Wei Yap},
title = {Identification of novel peroxisome proliferator-activated receptor-gamma
(PPAR{\(\gamma\)}) agonists using molecular modeling method},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {11},
pages = {1143--1151},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9791-6},
doi = {10.1007/S10822-014-9791-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GeeWRSKY14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GenhedenMCE14,
author = {Samuel Genheden and
Ana I. Cabedo Martinez and
Michael P. Criddle and
Jonathan W. Essex},
title = {Extensive all-atom Monte Carlo sampling and {QM/MM} corrections in
the {SAMPL4} hydration free energy challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {187--200},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9717-3},
doi = {10.1007/S10822-014-9717-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GenhedenMCE14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GibbG14,
author = {Corinne L. D. Gibb and
Bruce C. Gibb},
title = {Binding of cyclic carboxylates to octa-acid deep-cavity cavitand},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {319--325},
year = {2014},
url = {https://doi.org/10.1007/s10822-013-9690-2},
doi = {10.1007/S10822-013-9690-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GibbG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Guthrie14,
author = {J. Peter Guthrie},
title = {SAMPL4, a blind challenge for computational solvation free energies:
the compounds considered},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {151--168},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9738-y},
doi = {10.1007/S10822-014-9738-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Guthrie14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HenzlerUHR14,
author = {Angela M. Henzler and
Sascha Urbaczek and
Matthias Hilbig and
Matthias Rarey},
title = {An integrated approach to knowledge-driven structure-based virtual
screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {9},
pages = {927--939},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9769-4},
doi = {10.1007/S10822-014-9769-4},
timestamp = {Wed, 10 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HenzlerUHR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HoguesSP14,
author = {Herv{\'{e}} Hogues and
Traian Sulea and
Enrico O. Purisima},
title = {Exhaustive docking and solvated interaction energy scoring: lessons
learned from the {SAMPL4} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {417--427},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9715-5},
doi = {10.1007/S10822-014-9715-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HoguesSP14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HongCWSCYBBCBEYQLCWZHQCH14,
author = {Xuan Hong and
Ping Cao and
Yoshiaki Washio and
Graham Simpson and
Nino Campobasso and
Jingsong Yang and
Jennifer Borthwick and
George Burton and
Julien Chabanet and
Sophie Bertrand and
Helen Evans and
Robert J. Young and
Junya Qu and
Hu Li and
Josh Cottom and
Paris Ward and
Hong Zhang and
Thau Ho and
Donghui Qin and
Siegfried Christensen and
Martha S. Head},
title = {Structure-guided optimization of small molecule c-Abl activators},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {2},
pages = {75--87},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9731-5},
doi = {10.1007/S10822-014-9731-5},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HongCWSCYBBCBEYQLCWZHQCH14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HsiaoS14,
author = {Ya{-}Wen Hsiao and
P{\"{a}}r S{\"{o}}derhjelm},
title = {Prediction of {SAMPL4} host-guest binding affinities using funnel
metadynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {443--454},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9724-4},
doi = {10.1007/S10822-014-9724-4},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HsiaoS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HsuHWHL14,
author = {Justin Bo{-}Kai Hsu and
Kai{-}Yao Huang and
Julia Tzu{-}Ya Weng and
Chien{-}Hsun Huang and
Tzong{-}Yi Lee},
title = {Incorporating significant amino acid pairs and protein domains to
predict {RNA} splicing-related proteins with functional roles},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {1},
pages = {49--60},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9706-6},
doi = {10.1007/S10822-014-9706-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HsuHWHL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HuLSMSJ14,
author = {Xin Hu and
Patricia M. Legler and
Noel Southall and
David J. Maloney and
Anton Simeonov and
Ajit Jadhav},
title = {Structural insight into exosite binding and discovery of novel exosite
inhibitors of botulinum neurotoxin serotype {A} through in silico
screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {7},
pages = {765--778},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9758-7},
doi = {10.1007/S10822-014-9758-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HuLSMSJ14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JiangXLPHZSY14,
author = {Zhengyu Jiang and
Li{-}Li Xu and
Meng{-}Chen Lu and
Yang Pan and
Hao{-}Ze Huang and
Xiao{-}Jin Zhang and
Hao{-}Peng Sun and
Qidong You},
title = {Investigation of the intermolecular recognition mechanism between
the {E3} ubiquitin ligase Keap1 and substrate based on multiple substrates
analysis},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {12},
pages = {1233--1245},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9799-y},
doi = {10.1007/S10822-014-9799-Y},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JiangXLPHZSY14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KalinicZE14,
author = {Marko Kalinic and
Mire Zloh and
Slavica Eric},
title = {Structural insights into binding of small molecule inhibitors to Enhancer
of Zeste Homolog 2},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {11},
pages = {1109--1128},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9788-1},
doi = {10.1007/S10822-014-9788-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KalinicZE14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KamstraDWCPF14,
author = {Rhiannon L. Kamstra and
Saedeh Dadgar and
John Wigg and
Morshed A. Chowdhury and
Christopher P. Phenix and
Wely B. Floriano},
title = {Creating and virtually screening databases of fluorescently-labelled
compounds for the discovery of target-specific molecular probes},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {11},
pages = {1129--1142},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9789-0},
doi = {10.1007/S10822-014-9789-0},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KamstraDWCPF14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KennyLM14,
author = {Peter W. Kenny and
Andrei Leit{\~{a}}o and
Carlos A. Montanari},
title = {Ligand efficiency metrics considered harmful},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {7},
pages = {699--710},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9757-8},
doi = {10.1007/S10822-014-9757-8},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KennyLM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KhanATHZNRPAC14,
author = {Khalid M. Khan and
Nida Ambreen and
Muhammad Taha and
Sobia Ahsan Halim and
Zaheer{-}ul{-}Haq and
Shagufta Naureen and
Saima Rasheed and
Shahnaz Perveen and
Sajjad Ali and
Mohammad Iqbal Choudhary},
title = {Structure-based design, synthesis and biological evaluation of {\(\beta\)}-glucuronidase
inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {5},
pages = {577--585},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9745-z},
doi = {10.1007/S10822-014-9745-Z},
timestamp = {Sun, 19 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KhanATHZNRPAC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KimG14,
author = {Soo{-}Kyung Kim and
William A. Goddard III},
title = {Predicted 3D structures of olfactory receptors with details of odorant
binding to {OR1G1}},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {12},
pages = {1175--1190},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9793-4},
doi = {10.1007/S10822-014-9793-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KimG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KireevaOKKT14,
author = {Natalia V. Kireeva and
Svetlana I. Ovchinnikova and
Sergey L. Kuznetsov and
Andrey M. Kazennov and
Aslan Yu. Tsivadze},
title = {Impact of distance-based metric learning on classification and visualization
model performance and structure-activity landscapes},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {2},
pages = {61--73},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9719-1},
doi = {10.1007/S10822-014-9719-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KireevaOKKT14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KonigPMB14,
author = {Gerhard K{\"{o}}nig and
Frank C. Pickard IV and
Ye Mei and
Bernard R. Brooks},
title = {Predicting hydration free energies with a hybrid {QM/MM} approach:
an evaluation of implicit and explicit solvation models in {SAMPL4}},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {245--257},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9708-4},
doi = {10.1007/S10822-014-9708-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KonigPMB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KopecK14,
author = {Wojciech Kopec and
Himanshu Khandelia},
title = {Reinforcing the membrane-mediated mechanism of action of the anti-tuberculosis
candidate drug thioridazine with molecular simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {2},
pages = {123--134},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9737-z},
doi = {10.1007/S10822-014-9737-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KopecK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KoziaraSMM14,
author = {Katarzyna B. Koziara and
Martin Stroet and
Alpeshkumar K. Malde and
Alan E. Mark},
title = {Testing and validation of the Automated Topology Builder {(ATB)} version
2.0: prediction of hydration free enthalpies},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {221--233},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9713-7},
doi = {10.1007/S10822-014-9713-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KoziaraSMM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KrizAMZCWK14,
author = {Zdenek Kr{\'{\i}}z and
Jan Adam and
Jana Mr{\'{a}}zkov{\'{a}} and
Petros Zotos and
Thomais Chatzipavlou and
Michaela Wimmerov{\'{a}} and
Jaroslav Koca},
title = {Engineering the Pseudomonas aeruginosa {II} lectin: designing mutants
with changed affinity and specificity},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {9},
pages = {951--960},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9774-7},
doi = {10.1007/S10822-014-9774-7},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KrizAMZCWK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KumarKGRMAS14,
author = {Vikash Kumar and
Saman Khan and
Priyanka Gupta and
Namrata Rastogi and
Durga Prasad Mishra and
Shakil Ahmed and
Mohammad Imran Siddiqi},
title = {Identification of novel inhibitors of human Chk1 using pharmacophore-based
virtual screening and their evaluation as potential anti-cancer agents},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {12},
pages = {1247--1256},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9800-9},
doi = {10.1007/S10822-014-9800-9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KumarKGRMAS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiDF14,
author = {Libo Li and
Ken A. Dill and
Christopher J. Fennell},
title = {Testing the semi-explicit assembly model of aqueous solvation in the
{SAMPL4} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {259--264},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9712-8},
doi = {10.1007/S10822-014-9712-8},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LiDF14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuZYGGTMLX14,
author = {Zhihong Liu and
Minghao Zheng and
Xin Yan and
Qiong Gu and
Johann Gasteiger and
Johan Tijhuis and
Peter Maas and
Jiabo Li and
Jun Xu},
title = {ChemStable: a web server for rule-embedded na{\"{\i}}ve Bayesian
learning approach to predict compound stability},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {9},
pages = {941--950},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9778-3},
doi = {10.1007/S10822-014-9778-3},
timestamp = {Wed, 09 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LiuZYGGTMLX14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LounnasWNSHNPTV14,
author = {Val{\`{e}}re Lounnas and
Henry B. Wedler and
Timothy Newman and
Gijs Schaftenaar and
Jason G. Harrison and
Gabriella Nepomuceno and
Ryan Pemberton and
Dean J. Tantillo and
Gert Vriend},
title = {Visually impaired researchers get their hands on quantum chemistry:
application to a computational study on the isomerization of a sterol},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {11},
pages = {1057--1067},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9782-7},
doi = {10.1007/S10822-014-9782-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LounnasWNSHNPTV14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LuoGZMLL14,
author = {Jiesi Luo and
Yanzhi Guo and
Yun Zhong and
Duo Ma and
Wenling Li and
Menglong Li},
title = {A functional feature analysis on diverse protein-protein interactions:
application for the prediction of binding affinity},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {6},
pages = {619--629},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9746-y},
doi = {10.1007/S10822-014-9746-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LuoGZMLL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MaggioraB14,
author = {Gerald M. Maggiora and
J{\"{u}}rgen Bajorath},
title = {Chemical space networks: a powerful new paradigm for the description
of chemical space},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {8},
pages = {795--802},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9760-0},
doi = {10.1007/S10822-014-9760-0},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MaggioraB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MaiC14,
author = {Te{-}Lun Mai and
Chi{-}Ming Chen},
title = {Computational prediction of kink properties of helices in membrane
proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {2},
pages = {99--109},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9734-2},
doi = {10.1007/S10822-014-9734-2},
timestamp = {Fri, 28 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/MaiC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ManzoniS14,
author = {Francesco Manzoni and
P{\"{a}}r S{\"{o}}derhjelm},
title = {Prediction of hydration free energies for the {SAMPL4} data set with
the {AMOEBA} polarizable force field},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {235--244},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9733-3},
doi = {10.1007/S10822-014-9733-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ManzoniS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/McEwenL14,
author = {Leah McEwen and
Ye Li},
title = {Academic librarians at play in the field of cheminformatics: building
the case for chemistry research data management},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {10},
pages = {975--988},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9777-4},
doi = {10.1007/S10822-014-9777-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/McEwenL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/McGaugheyBCSBBPBC14,
author = {Georgia B. McGaughey and
Christopher I. Bayly and
Christopher D. Cox and
John D. Schreier and
Michael J. Breslin and
Michael Bogusky and
Steve Pitzenberger and
Richard Ball and
Paul J. Coleman},
title = {Shaping suvorexant: application of experimental and theoretical methods
for driving synthetic designs},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {1},
pages = {5--12},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9710-x},
doi = {10.1007/S10822-014-9710-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/McGaugheyBCSBBPBC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MikulskisCAKBGMSR14,
author = {Paulius Mikulskis and
Daniela Cioloboc and
Milica Andrejic and
Sakshi Khare and
Joakim Brorsson and
Samuel Genheden and
Ricardo A. Mata and
P{\"{a}}r S{\"{o}}derhjelm and
Ulf Ryde},
title = {Free-energy perturbation and quantum mechanical study of {SAMPL4}
octa-acid host-guest binding energies},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {375--400},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9739-x},
doi = {10.1007/S10822-014-9739-X},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MikulskisCAKBGMSR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MobleyG14,
author = {David L. Mobley and
J. Peter Guthrie},
title = {FreeSolv: a database of experimental and calculated hydration free
energies, with input files},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {7},
pages = {711--720},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9747-x},
doi = {10.1007/S10822-014-9747-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MobleyG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MobleyLLWPFDSBO14,
author = {David L. Mobley and
Shuai Liu and
Nathan M. Lim and
Karisa L. Wymer and
Alexander L. Perryman and
Stefano Forli and
Nan{-}Jie Deng and
Justin Su and
Kim Branson and
Arthur J. Olson},
title = {Blind prediction of {HIV} integrase binding from the {SAMPL4} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {327--345},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9723-5},
doi = {10.1007/S10822-014-9723-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MobleyLLWPFDSBO14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MobleyWLG14,
author = {David L. Mobley and
Karisa L. Wymer and
Nathan M. Lim and
J. Peter Guthrie},
title = {Blind prediction of solvation free energies from the {SAMPL4} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {135--150},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9718-2},
doi = {10.1007/S10822-014-9718-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MobleyWLG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MonroeS14,
author = {Jacob I. Monroe and
Michael R. Shirts},
title = {Converging free energies of binding in cucurbit[7]uril and octa-acid
host-guest systems from {SAMPL4} using expanded ensemble simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {401--415},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9716-4},
doi = {10.1007/S10822-014-9716-4},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MonroeS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MuddanaFMG14,
author = {Hari S. Muddana and
Andrew T. Fenley and
David L. Mobley and
Michael K. Gilson},
title = {The {SAMPL4} host-guest blind prediction challenge: an overview},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {305--317},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9735-1},
doi = {10.1007/S10822-014-9735-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MuddanaFMG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MuddanaSFG14,
author = {Hari S. Muddana and
Neil V. Sapra and
Andrew T. Fenley and
Michael K. Gilson},
title = {The {SAMPL4} hydration challenge: evaluation of partial charge sets
with explicit-water molecular dynamics simulations},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {277--287},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9714-6},
doi = {10.1007/S10822-014-9714-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MuddanaSFG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MuddanaYSFG14,
author = {Hari S. Muddana and
Jian Yin and
Neil V. Sapra and
Andrew T. Fenley and
Michael K. Gilson},
title = {Blind prediction of {SAMPL4} cucurbit[7]uril binding affinities with
the mining minima method},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {463--474},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9726-2},
doi = {10.1007/S10822-014-9726-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MuddanaYSFG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MukherjeeKB14,
author = {Sanchita Mukherjee and
Sangeeta Kundu and
Dhananjay Bhattacharyya},
title = {Temperature effect on poly(dA).poly(dT): molecular dynamics simulation
studies of polymeric and oligomeric constructs},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {7},
pages = {735--749},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9755-x},
doi = {10.1007/S10822-014-9755-X},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MukherjeeKB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NemethSNHGO14,
author = {Eszter N{\'{e}}meth and
Gabriella K. Schilli and
G{\'{a}}bor Nagy and
Christoph Hasenhindl and
B{\'{e}}la Gyurcsik and
Chris Oostenbrink},
title = {Design of a colicin {E7} based chimeric zinc-finger nuclease},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {8},
pages = {841--850},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9765-8},
doi = {10.1007/S10822-014-9765-8},
timestamp = {Wed, 06 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NemethSNHGO14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NeumannB14,
author = {Janna Neumann and
Jan Brase},
title = {DataCite and {DOI} names for research data},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {10},
pages = {1035--1041},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9776-5},
doi = {10.1007/S10822-014-9776-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NeumannB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Nicholls14,
author = {Anthony Nicholls},
title = {{JCAMD} special series: statistics and molecular modeling},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {9},
pages = {885--886},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9781-8},
doi = {10.1007/S10822-014-9781-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Nicholls14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Nicholls14a,
author = {Anthony Nicholls},
title = {Confidence limits, error bars and method comparison in molecular modeling.
Part 1: The calculation of confidence intervals},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {9},
pages = {887--918},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9753-z},
doi = {10.1007/S10822-014-9753-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Nicholls14a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OberhauserNC14,
author = {Nils Oberhauser and
Alessandra Nurisso and
Pierre{-}Alain Carrupt},
title = {{MLP} Tools: a PyMOL plugin for using the molecular lipophilicity
potential in computer-aided drug design},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {5},
pages = {587--596},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9744-0},
doi = {10.1007/S10822-014-9744-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OberhauserNC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParameswaranM14,
author = {Sreeja Parameswaran and
David L. Mobley},
title = {Box size effects are negligible for solvation free energies of neutral
solutes},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {8},
pages = {825--829},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9766-7},
doi = {10.1007/S10822-014-9766-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ParameswaranM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Park14,
author = {Hwangseo Park},
title = {Extended solvent-contact model approach to {SAMPL4} blind prediction
challenge for hydration free energies},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {175--186},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9729-z},
doi = {10.1007/S10822-014-9729-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Park14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParvizpourRRIS14,
author = {Sepideh Parvizpour and
Jafar Razmara and
Aizi Nor Mazila Ramli and
Rosli Md. Illias and
Mohd Shahir Shamsir},
title = {Structural and functional analysis of a novel psychrophilic {\(\beta\)}-mannanase
from Glaciozyma antarctica {PI12}},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {6},
pages = {685--698},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9751-1},
doi = {10.1007/S10822-014-9751-1},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ParvizpourRRIS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PatilBK14,
author = {Sachin P. Patil and
Pedro J. Ballester and
Cassidy R. Kerezsi},
title = {Prospective virtual screening for novel p53-MDM2 inhibitors using
ultrafast shape recognition},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {2},
pages = {89--97},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9732-4},
doi = {10.1007/S10822-014-9732-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PatilBK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PeatDNMD14,
author = {Thomas S. Peat and
Olan Dolezal and
Janet Newman and
David L. Mobley and
John J. Deadman},
title = {Interrogating {HIV} integrase for compounds that bind- a {SAMPL} challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {347--362},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9721-7},
doi = {10.1007/S10822-014-9721-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PeatDNMD14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Perez-GallegosGGL14,
author = {Ayax P{\'{e}}rez{-}Gallegos and
Mireia Garcia{-}Viloca and
{\`{A}}ngels Gonz{\'{a}}lez{-}Lafont and
Jos{\'{e}} M. Lluch},
title = {A {QM/MM} study of the associative mechanism for the phosphorylation
reaction catalyzed by protein kinase {A} and its {D166A} mutant},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {11},
pages = {1077--1091},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9786-3},
doi = {10.1007/S10822-014-9786-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Perez-GallegosGGL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PerrymanSFSO14,
author = {Alexander L. Perryman and
Daniel N. Santiago and
Stefano Forli and
Diogo Santos{-}Martins and
Arthur J. Olson},
title = {Virtual screening with AutoDock Vina and the common pharmacophore
engine of a low diversity library of fragments and hits against the
three allosteric sites of {HIV} integrase: participation in the {SAMPL4}
protein-ligand binding challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {429--441},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9709-3},
doi = {10.1007/S10822-014-9709-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PerrymanSFSO14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PingaliHMBBCB14,
author = {Pavan Kumar Pingali and
Sukanya Halder and
Debasish Mukherjee and
Sankar Basu and
Rahul Banerjee and
Devapriya Choudhury and
Dhananjay Bhattacharyya},
title = {Analysis of stacking overlap in nucleic acid structures: algorithm
and application},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {8},
pages = {851--867},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9767-6},
doi = {10.1007/S10822-014-9767-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PingaliHMBBCB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PraditwongwanCSWLNHMBCT14,
author = {Warachai Praditwongwan and
Phimonphan Chuankhayan and
Somphot Saoin and
Tanchanok Wisitponchai and
Vannajan Sanghiran Lee and
Sawitree Nangola and
Saw See Hong and
Philippe Minard and
Pierre Boulanger and
Chun{-}Jung Chen and
Chatchai Tayapiwatana},
title = {Crystal structure of an antiviral ankyrin targeting the {HIV-1} capsid
and molecular modeling of the ankyrin-capsid complex},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {8},
pages = {869--884},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9772-9},
doi = {10.1007/S10822-014-9772-9},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/PraditwongwanCSWLNHMBCT14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ReinischK14,
author = {Jens Reinisch and
Andreas Klamt},
title = {Prediction of free energies of hydration with {COSMO-RS} on the {SAMPL4}
data set},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {169--173},
year = {2014},
url = {https://doi.org/10.1007/s10822-013-9701-3},
doi = {10.1007/S10822-013-9701-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ReinischK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Saavedra-VelezCMGBCGTR14,
author = {Margarita Virginia Saavedra{-}V{\'{e}}lez and
Jos{\'{e}} Correa{-}Basurto and
Myrna H. Matus and
Eloy Gasca{-}P{\'{e}}rez and
Martiniano Bello and
Roberto Cuevas{-}Hern{\'{a}}ndez and
Rosa Virginia Garc{\'{\i}}a{-}Rodr{\'{\i}}guez and
Jos{\'{e}} G. Trujillo{-}Ferrara and
Fernando Rafael Ramos{-}Morales},
title = {Seeking potential anticonvulsant agents that target {GABAA} receptors
using experimental and theoretical procedures},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {12},
pages = {1217--1232},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9798-z},
doi = {10.1007/S10822-014-9798-Z},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Saavedra-VelezCMGBCGTR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Saeed0SS14,
author = {Faisal Saeed and
Ali Ahmed and
Mohd Shahir Shamsir and
Naomie Salim},
title = {Weighted voting-based consensus clustering for chemical structure
databases},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {6},
pages = {675--684},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9750-2},
doi = {10.1007/S10822-014-9750-2},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Saeed0SS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Sandberg14,
author = {Lars Sandberg},
title = {Predicting hydration free energies with chemical accuracy: the {SAMPL4}
challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {3},
pages = {211--219},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9725-3},
doi = {10.1007/S10822-014-9725-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Sandberg14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SantoshiN14,
author = {Seneha Santoshi and
Pradeep K. Naik},
title = {Molecular insight of isotypes specific {\(\beta\)}-tubulin interaction
of tubulin heterodimer with noscapinoids},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {7},
pages = {751--763},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9756-9},
doi = {10.1007/S10822-014-9756-9},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SantoshiN14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SarmahR14,
author = {Amrit Sarmah and
Ram Kinkar Roy},
title = {A density functional reactivity theory {(DFRT)} based approach to
understand the interaction of cisplatin analogues with protecting
agents},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {12},
pages = {1153--1173},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9790-7},
doi = {10.1007/S10822-014-9790-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SarmahR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Slater14,
author = {Anthony Michael Slater},
title = {The {IUPAC} aqueous and non-aqueous experimental pKa data repositories
of organic acids and bases},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {10},
pages = {1031--1034},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9764-9},
doi = {10.1007/S10822-014-9764-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Slater14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SolovevVT14,
author = {Vitaly P. Solov'ev and
Alexandre Varnek and
Aslan Yu. Tsivadze},
title = {{QSPR} ensemble modelling of the 1: 1 and 1: 2 complexation of Co2+,
Ni2+, and Cu2+ with organic ligands: relationships between stability
constants},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {5},
pages = {549--564},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9741-3},
doi = {10.1007/S10822-014-9741-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SolovevVT14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SpragueSKZSITLZ14,
author = {Brienne Sprague and
Qian Shi and
Marlene T. Kim and
Liying Zhang and
Alexander Sedykh and
Eiichiro Ichiishi and
Harukuni Tokuda and
Kuo{-}Hsiung Lee and
Hao Zhu},
title = {Design, synthesis and experimental validation of novel potential chemopreventive
agents using random forest and support vector machine binary classifiers},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {6},
pages = {631--646},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9748-9},
doi = {10.1007/S10822-014-9748-9},
timestamp = {Fri, 10 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SpragueSKZSITLZ14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SuriHJN14,
author = {Charu Suri and
Triscia W. Hendrickson and
Harish C. Joshi and
Pradeep Kumar Naik},
title = {Molecular insight into {\(\gamma\)}-{\(\gamma\)} tubulin lateral interactions
within the {\(\gamma\)}-tubulin ring complex ({\(\gamma\)}-TuRC)},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {9},
pages = {961--972},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9779-2},
doi = {10.1007/S10822-014-9779-2},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SuriHJN14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TahaHK14,
author = {Mutasem O. Taha and
Maha Habash and
Mohammad A. Khanfar},
title = {The use of docking-based comparative intermolecular contacts analysis
to identify optimal docking conditions within glucokinase and to discover
of new {GK} activators},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {5},
pages = {509--547},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9740-4},
doi = {10.1007/S10822-014-9740-4},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/TahaHK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ThakralB14,
author = {Priyanka Thakral and
A. K. Bakhshi},
title = {Computational atomistic blueprinting of novel conducting copolymers
using particle swarm optimization},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {2},
pages = {111--122},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9736-0},
doi = {10.1007/S10822-014-9736-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ThakralB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TsvetkovS14,
author = {Vladimir B. Tsvetkov and
Alexander V. Serbin},
title = {Molecular dynamics modeling the synthetic and biological polymers
interactions pre-studied via docking - Anchors modified polyanions
interference with the {HIV-1} fusion mediator},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {6},
pages = {647--673},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9749-8},
doi = {10.1007/S10822-014-9749-8},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/TsvetkovS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VoetKBZ14,
author = {Arnout R. D. Voet and
Ashutosh Kumar and
Francois Berenger and
Kam Y. J. Zhang},
title = {Combining in silico and in cerebro approaches for virtual screening
and pose prediction in {SAMPL4}},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {4},
pages = {363--373},
year = {2014},
url = {https://doi.org/10.1007/s10822-013-9702-2},
doi = {10.1007/S10822-013-9702-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VoetKBZ14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WangTNJ14,
author = {Huei{-}Tang Wang and
Fadlilatul Taufany and
Santhanamoorthi Nachimuthu and
Jyh{-}Chiang Jiang},
title = {Theoretical studies on effective metal-to-ligand charge transfer characteristics
of novel ruthenium dyes for dye sensitized solar cells},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {5},
pages = {565--575},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9742-2},
doi = {10.1007/S10822-014-9742-2},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WangTNJ14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Warr14,
author = {Wendy A. Warr},
title = {Data sharing matters},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {1},
pages = {1--4},
year = {2014},
url = {https://doi.org/10.1007/s10822-013-9705-z},
doi = {10.1007/S10822-013-9705-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Warr14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Warr14a,
author = {Wendy A. Warr},
title = {Data sharing as an issue},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {10},
pages = {973--974},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9796-1},
doi = {10.1007/S10822-014-9796-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Warr14a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WendtC14,
author = {Bernd Wendt and
Richard D. Cramer},
title = {Challenging the gold standard for 3D-QSAR: template CoMFA versus X-ray
alignment},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {8},
pages = {803--824},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9761-z},
doi = {10.1007/S10822-014-9761-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WendtC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WilliamsT14,
author = {Antony J. Williams and
Valery Tkachenko},
title = {The Royal Society of Chemistry and the delivery of chemistry data
repositories for the community},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {10},
pages = {1023--1030},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9784-5},
doi = {10.1007/S10822-014-9784-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WilliamsT14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WolfSBAK14,
author = {Antje Wolf and
Sebastian Schoof and
Sascha Baumann and
Hans{-}Dieter Arndt and
Karl N. Kirschner},
title = {Structure-activity relationships of thiostrepton derivatives: implications
for rational drug design},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {12},
pages = {1205--1215},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9797-0},
doi = {10.1007/S10822-014-9797-0},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/WolfSBAK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/XingRL14,
author = {Li Xing and
Brajesh Rai and
Elizabeth A. Lunney},
title = {Scaffold mining of kinase hinge binders in crystal structure database},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {1},
pages = {13--23},
year = {2014},
url = {https://doi.org/10.1007/s10822-013-9700-4},
doi = {10.1007/S10822-013-9700-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/XingRL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YuLRM14,
author = {Wenbo Yu and
Sirish Kaushik Lakkaraju and
E. Prabhu Raman and
Alexander D. MacKerell Jr.},
title = {Site-Identification by Ligand Competitive Saturation {(SILCS)} assisted
pharmacophore modeling},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {5},
pages = {491--507},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9728-0},
doi = {10.1007/S10822-014-9728-0},
timestamp = {Wed, 09 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/YuLRM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhangVB14,
author = {Bijun Zhang and
Martin Vogt and
J{\"{u}}rgen Bajorath},
title = {Design of an activity landscape view taking compound-based feature
probabilities into account},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {9},
pages = {919--926},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9773-8},
doi = {10.1007/S10822-014-9773-8},
timestamp = {Mon, 30 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ZhangVB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZorganiPD14,
author = {Mohamed Amine Zorgani and
Kevin Patron and
Micka{\"{e}}l Desvaux},
title = {New insight in the structural features of haloadaptation in {\(\alpha\)}-amylases
from halophilic Archaea following homology modeling strategy: folded
and stable conformation maintained through low hydrophobicity and
highly negative charged surface},
journal = {J. Comput. Aided Mol. Des.},
volume = {28},
number = {7},
pages = {721--734},
year = {2014},
url = {https://doi.org/10.1007/s10822-014-9754-y},
doi = {10.1007/S10822-014-9754-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZorganiPD14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AbuhamdahHT13,
author = {Sawsan Abuhamdah and
Maha Habash and
Mutasem O. Taha},
title = {Elaborate ligand-based modeling coupled with {QSAR} analysis and in
silico screening reveal new potent acetylcholinesterase inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {12},
pages = {1075--1092},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9699-6},
doi = {10.1007/S10822-013-9699-6},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AbuhamdahHT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AnouarRBTBMHAIWT13,
author = {El Hassane Anouar and
Salwa Raweh and
Imene Bayach and
Muhammad Taha and
Mohd Syukri Baharudin and
Florent Di Meo and
Mizaton Hazizul Hasan and
Aishah Adam and
Nor Hadiani Ismail and
Jean{-}Fr{\'{e}}d{\'{e}}ric F. Weber and
Patrick Trouillas},
title = {Antioxidant properties of phenolic Schiff bases: structure-activity
relationship and mechanism of action},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {11},
pages = {951--964},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9692-0},
doi = {10.1007/S10822-013-9692-0},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AnouarRBTBMHAIWT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AshidaK13,
author = {Takeshi Ashida and
Takeshi Kikuchi},
title = {Estimation of relative binding free energy based on a free energy
variational principle for the FKBP-ligand system},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {6},
pages = {479--490},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9657-3},
doi = {10.1007/S10822-013-9657-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AshidaK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BaskinZ13,
author = {Igor I. Baskin and
Nelly I. Zhokhova},
title = {The continuous molecular fields approach to building 3D-QSAR models},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {5},
pages = {427--442},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9656-4},
doi = {10.1007/S10822-013-9656-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BaskinZ13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BrowningCS13,
author = {Michael R. Browning and
Bradley T. Calhoun and
Sanjay Joshua Swamidass},
title = {Managing missing measurements in small-molecule screens},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {5},
pages = {469--478},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9642-x},
doi = {10.1007/S10822-013-9642-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BrowningCS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BrylinskiF13,
author = {Michal Brylinski and
Wei Pan Feinstein},
title = {eFindSite: Improved prediction of ligand binding sites in protein
models using meta-threading, machine learning and auxiliary ligands},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {6},
pages = {551--567},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9663-5},
doi = {10.1007/S10822-013-9663-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BrylinskiF13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CadiaRM13,
author = {Marta Del Cadia and
Francesca De Rienzo and
Maria Cristina Menziani},
title = {Approaching the 5-HT3 receptor heterogeneity by computational studies
of the transmembrane and intracellular domains},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {6},
pages = {491--509},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9658-2},
doi = {10.1007/S10822-013-9658-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CadiaRM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChakrabortyMS13,
author = {Biprashekhar Chakraborty and
Raisa Mukherjee and
Jayati Sengupta},
title = {Structural insights into the mechanism of translational inhibition
by the fungicide sordarin},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {2},
pages = {173--184},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9636-8},
doi = {10.1007/S10822-013-9636-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChakrabortyMS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChangWLCHH13,
author = {Tzu{-}Hao Chang and
Li{-}Ching Wu and
Tzong{-}Yi Lee and
Shu{-}Pin Chen and
Hsien{-}Da Huang and
Jorng{-}Tzong Horng},
title = {EuLoc: a web-server for accurately predict protein subcellular localization
in eukaryotes by incorporating various features of sequence segments
into the general form of Chou's PseAAC},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {1},
pages = {91--103},
year = {2013},
url = {https://doi.org/10.1007/s10822-012-9628-0},
doi = {10.1007/S10822-012-9628-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChangWLCHH13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChenWZL13,
author = {Jianzhong Chen and
Jinan Wang and
Weiliang Zhu and
Guohui Li},
title = {A computational analysis of binding modes and conformation changes
of {MDM2} induced by p53 and inhibitor bindings},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {11},
pages = {965--974},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9693-z},
doi = {10.1007/S10822-013-9693-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChenWZL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CoxGLMP13,
author = {Richard Cox and
Darren V. S. Green and
Christopher N. Luscombe and
Noj Malcolm and
Stephen D. Pickett},
title = {{QSAR} workbench: automating {QSAR} modeling to drive compound design},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {4},
pages = {321--336},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9648-4},
doi = {10.1007/S10822-013-9648-4},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CoxGLMP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CrivelliLKM13,
author = {Joseph J. Crivelli and
Gordon Lemmon and
Kristian Kaufmann and
Jens Meiler},
title = {Simultaneous prediction of binding free energy and specificity for
{PDZ} domain-peptide interactions},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {12},
pages = {1051--1065},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9696-9},
doi = {10.1007/S10822-013-9696-9},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CrivelliLKM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DallanoceGPSMGFA13,
author = {Clelia Dallanoce and
Giovanni Grazioso and
Diego Yuri Pom{\`{e}} and
Miriam Sciaccaluga and
Carlo Matera and
Cecilia Gotti and
Sergio Fucile and
Marco De Amici},
title = {Investigating the hydrogen-bond acceptor site of the nicotinic pharmacophore
model: a computational and experimental study using epibatidine-related
molecular probes},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {11},
pages = {975--987},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9694-y},
doi = {10.1007/S10822-013-9694-Y},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DallanoceGPSMGFA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DebeMGMGM13,
author = {Derek A. Debe and
Ravindra B. Mamidipaka and
Robert J. Gregg and
James T. Metz and
Rishi R. Gupta and
Steven W. Muchmore},
title = {{ALOHA:} a novel probability fusion approach for scoring multi-parameter
drug-likeness during the lead optimization stage of drug discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {9},
pages = {771--782},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9679-x},
doi = {10.1007/S10822-013-9679-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DebeMGMGM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DebnathVJKP13,
author = {Utsab Debnath and
Saroj Verma and
Surabhi Jain and
Setu B. Katti and
Yenamandra S. Prabhakar},
title = {Pyridones as NNRTIs against {HIV-1} mutants: 3D-QSAR and protein informatics},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {7},
pages = {637--654},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9667-1},
doi = {10.1007/S10822-013-9667-1},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DebnathVJKP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DominguezVS13,
author = {Jos{\'{e}} L. Dom{\'{\i}}nguez and
M. Carmen Villaverde and
Fredy Sussman},
title = {Effect of pH and ligand charge state on {BACE-1} fragment docking
performance},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {5},
pages = {403--417},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9653-7},
doi = {10.1007/S10822-013-9653-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DominguezVS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DrwalAPG13,
author = {Malgorzata N. Drwal and
Keli Agama and
Yves Pommier and
Renate Griffith},
title = {Development of purely structure-based pharmacophores for the topoisomerase
I-DNA-ligand binding pocket},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {12},
pages = {1037--1049},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9695-x},
doi = {10.1007/S10822-013-9695-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DrwalAPG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/EbinaUK13,
author = {Teppei Ebina and
Yuki Umezawa and
Yutaka Kuroda},
title = {IS-Dom: a dataset of independent structural domains automatically
delineated from protein structures},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {5},
pages = {419--426},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9654-6},
doi = {10.1007/S10822-013-9654-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/EbinaUK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FernandezOF13,
author = {David Fern{\'{a}}ndez and
Joaqu{\'{\i}}n Ortega{-}Castro and
Juan Frau},
title = {Human farnesyl pyrophosphate synthase inhibition by nitrogen bisphosphonates:
a 3D-QSAR study},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {8},
pages = {739--754},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9674-2},
doi = {10.1007/S10822-013-9674-2},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FernandezOF13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GapsysGB13,
author = {Vytautas Gapsys and
Bert L. de Groot and
Rodolfo Briones},
title = {Computational analysis of local membrane properties},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {10},
pages = {845--858},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9684-0},
doi = {10.1007/S10822-013-9684-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GapsysGB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GochinWPB13,
author = {Miriam Gochin and
Landon R. Whitby and
Aaron H. Phillips and
Dale L. Boger},
title = {NMR-assisted computational studies of peptidomimetic inhibitors bound
in the hydrophobic pocket of {HIV-1} glycoprotein 41},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {7},
pages = {569--582},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9662-6},
doi = {10.1007/S10822-013-9662-6},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GochinWPB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GrafBHO13,
author = {Michael M. H. Graf and
Urban Bren and
Dietmar Haltrich and
Chris Oostenbrink},
title = {Molecular dynamics simulations give insight into d-glucose dioxidation
at {C2} and {C3} by Agaricus meleagris pyranose dehydrogenase},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {4},
pages = {295--304},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9645-7},
doi = {10.1007/S10822-013-9645-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GrafBHO13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Gupta-OstermannHB13,
author = {Disha Gupta{-}Ostermann and
Ye Hu and
J{\"{u}}rgen Bajorath},
title = {Systematic mining of analog series with related core structures in
multi-target activity space},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {8},
pages = {665--674},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9671-5},
doi = {10.1007/S10822-013-9671-5},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Gupta-OstermannHB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HuMB13,
author = {Ye Hu and
Gerald M. Maggiora and
J{\"{u}}rgen Bajorath},
title = {Activity cliffs in PubChem confirmatory bioassays taking inactive
compounds into account},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {2},
pages = {115--124},
year = {2013},
url = {https://doi.org/10.1007/s10822-012-9632-4},
doi = {10.1007/S10822-012-9632-4},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HuMB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JabeenWCPE13,
author = {Ishrat Jabeen and
Penpun Wetwitayaklung and
Peter Chiba and
Manuel Pastor and
Gerhard F. Ecker},
title = {2D- and 3D-QSAR studies of a series of benzopyranes and benzopyrano[3,
4b][1, 4]-oxazines as inhibitors of the multidrug transporter P-glycoprotein},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {2},
pages = {161--171},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9635-9},
doi = {10.1007/S10822-013-9635-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/JabeenWCPE13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JakubikRD13,
author = {Jan Jakubik and
Alena Rand{\'{a}}kov{\'{a}} and
Vladim{\'{\i}}r Dolezal},
title = {On homology modeling of the {M2} muscarinic acetylcholine receptor
subtype},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {6},
pages = {525--538},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9660-8},
doi = {10.1007/S10822-013-9660-8},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JakubikRD13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JarmulaR13,
author = {Adam Jarmula and
Wojciech Rode},
title = {Computational study of the effects of protein tyrosine nitrations
on the catalytic activity of human thymidylate synthase},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {1},
pages = {45--66},
year = {2013},
url = {https://doi.org/10.1007/s10822-012-9624-4},
doi = {10.1007/S10822-012-9624-4},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/JarmulaR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JerezJGBC13,
author = {Ma Jos{\'{e}} Jerez and
Miguel Jerez and
Coral Gonz{\'{a}}lez{-}Garc{\'{\i}}a and
Sara Ballester and
Ana Castro},
title = {Combined use of pharmacophoric models together with drug metabolism
and genotoxicity "in silico" studies in the hit finding process},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {1},
pages = {79--90},
year = {2013},
url = {https://doi.org/10.1007/s10822-012-9627-1},
doi = {10.1007/S10822-012-9627-1},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/JerezJGBC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Jimenez-LopezKHGA13,
author = {Jose C. Jimenez{-}Lopez and
Simeon O. Kotchoni and
Maria C. Hernandez{-}Soriano and
Emma W. Gachomo and
Juan D. Alch{\'{e}}},
title = {Structural functionality, catalytic mechanism modeling and molecular
allergenicity of phenylcoumaran benzylic ether reductase, an olive
pollen (Ole e 12) allergen},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {10},
pages = {873--895},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9686-y},
doi = {10.1007/S10822-013-9686-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Jimenez-LopezKHGA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KandeelK13,
author = {Mahmoud Kandeel and
Yukio Kitade},
title = {In silico molecular docking analysis of the human Argonaute 2 {PAZ}
domain reveals insights into {RNA} interference},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {7},
pages = {605--614},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9665-3},
doi = {10.1007/S10822-013-9665-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KandeelK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KarabulutNL13,
author = {Sedat Karabulut and
Hilmi Namli and
Jerzy Leszczynski},
title = {Detection of tautomer proportions of dimedone in solution: a new approach
based on theoretical and {FT-IR} viewpoint},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {8},
pages = {681--688},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9669-z},
doi = {10.1007/S10822-013-9669-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KarabulutNL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KaramanGDSHAMB13,
author = {Rafik Karaman and
Hiba Ghareeb and
Khuloud Kamal Dajani and
Laura Scrano and
Hussein Hallak and
Saleh Abu{-}Lafi and
Gennaro Mecca and
Sabino A. Bufo},
title = {Design, synthesis and in vitro kinetic study of tranexamic acid prodrugs
for the treatment of bleeding conditions},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {7},
pages = {615--635},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9666-2},
doi = {10.1007/S10822-013-9666-2},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KaramanGDSHAMB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KennyM13,
author = {Peter W. Kenny and
Carlos A. Montanari},
title = {Inflation of correlation in the pursuit of drug-likeness},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {1},
pages = {1--13},
year = {2013},
url = {https://doi.org/10.1007/s10822-012-9631-5},
doi = {10.1007/S10822-012-9631-5},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KennyM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KennyMP13,
author = {Peter W. Kenny and
Carlos A. Montanari and
Igor M. Prokopczyk},
title = {ClogPalk: a method for predicting alkane/water partition coefficient},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {5},
pages = {389--402},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9655-5},
doi = {10.1007/S10822-013-9655-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KennyMP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KennyMPSS13,
author = {Peter W. Kenny and
Carlos A. Montanari and
Igor M. Prokopczyk and
Fernanda A. Sala and
Geraldo Rodrigues Sartori},
title = {Automated molecule editing in molecular design},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {8},
pages = {655--664},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9676-0},
doi = {10.1007/S10822-013-9676-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KennyMPSS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KimNWM13,
author = {Meekyum Olivia Kim and
Sara E. Nichols and
Yi Wang and
James Andrew McCammon},
title = {Effects of histidine protonation and rotameric states on virtual screening
of M. tuberculosis RmlC},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {3},
pages = {235--246},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9643-9},
doi = {10.1007/S10822-013-9643-9},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KimNWM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KlimovichM13,
author = {Pavel V. Klimovich and
David L. Mobley},
title = {Erratum to: Predicting hydration free energies using all-atom molecular
dynamics simulations and multiple starting conformations},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {1},
pages = {105},
year = {2013},
url = {https://doi.org/10.1007/s10822-012-9622-6},
doi = {10.1007/S10822-012-9622-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KlimovichM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiuWLARSJLM13,
author = {Shuai Liu and
Yujie Wu and
Teng Lin and
Robert Abel and
Jonathan P. Redmann and
Christopher M. Summa and
Vivian R. Jaber and
Nathan M. Lim and
David L. Mobley},
title = {Lead optimization mapper: automating free energy calculations for
lead optimization},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {9},
pages = {755--770},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9678-y},
doi = {10.1007/S10822-013-9678-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiuWLARSJLM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LupyanAS13,
author = {Dmitry Lupyan and
Yuriy A. Abramov and
Woody Sherman},
title = {Erratum to: Close intramolecular sulfur-oxygen contacts: modified
force field parameters for improved conformation generation},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {3},
pages = {293},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9633-y},
doi = {10.1007/S10822-013-9633-Y},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LupyanAS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MalacB13,
author = {Kamil Mal{\'{a}}c and
Ivan Barv{\'{\i}}k},
title = {Substrate recognition by norovirus polymerase: microsecond molecular
dynamics study},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {4},
pages = {373--388},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9652-8},
doi = {10.1007/S10822-013-9652-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MalacB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MaloPSLB13,
author = {Marcus Malo and
Ronnie Persson and
Peder Svensson and
Kristina Luthman and
Lars Brive},
title = {Development of 7TM receptor-ligand complex models using ligand-biased,
semi-empirical helix-bundle repacking in torsion space: application
to the agonist interaction of the human dopamine {D2} receptor},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {3},
pages = {277--291},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9640-z},
doi = {10.1007/S10822-013-9640-Z},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/MaloPSLB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Marshall13,
author = {Garland R. Marshall},
title = {Limiting assumptions in molecular modeling: electrostatics},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {2},
pages = {107--114},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9634-x},
doi = {10.1007/S10822-013-9634-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Marshall13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MugumbateNRGMCG13,
author = {Grace Mugumbate and
Ana S. Newton and
Philip J. Rosenthal and
Jiri Gut and
Rui Moreira and
Kelly Chibale and
Rita C. Guedes},
title = {Novel anti-Plasmodial hits identified by virtual screening of the
{ZINC} database},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {10},
pages = {859--871},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9685-z},
doi = {10.1007/S10822-013-9685-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MugumbateNRGMCG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MulrooneyLQYMAMAMMBCBDDTS13,
author = {Carol A. Mulrooney and
David L. Lahr and
Michael J. Quintin and
Willmen Youngsaye and
Dennis Moccia and
Jacob K. Asiedu and
Evan L. Mulligan and
Lakshmi B. Akella and
Lisa A. Marcaurelle and
Philip Montgomery and
Joshua A. Bittker and
Paul A. Clemons and
Steve Brudz and
Sivaraman Dandapani and
Jeremy R. Duvall and
Nicola J. Tolliday and
Andrea de Souza},
title = {An informatic pipeline for managing high-throughput screening experiments
and analyzing data from stereochemically diverse libraries},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {5},
pages = {455--468},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9641-y},
doi = {10.1007/S10822-013-9641-Y},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MulrooneyLQYMAMAMMBCBDDTS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NgoNCFG13,
author = {Tony Ngo and
Timothy J. Nicholas and
Junli Chen and
Angela M. Finch and
Renate Griffith},
title = {5-HT1A receptor pharmacophores to screen for off-target activity of
{\(\alpha\)}1-adrenoceptor antagonists},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {4},
pages = {305--319},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9647-5},
doi = {10.1007/S10822-013-9647-5},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NgoNCFG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NilarMK13,
author = {Shahul H. Nilar and
Ngai Ling Ma and
Thomas H. Keller},
title = {The importance of molecular complexity in the design of screening
libraries},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {9},
pages = {783--792},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9683-1},
doi = {10.1007/S10822-013-9683-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NilarMK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OlabyAHCVB13,
author = {Reem Al Olaby and
Hassan M. Azzazy and
Rodney Harris and
Brett Chromy and
Jost Vielmetter and
Rod Balhorn},
title = {Identification of ligands that target the {HCV-E2} binding site on
{CD81}},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {4},
pages = {337--346},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9649-3},
doi = {10.1007/S10822-013-9649-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/OlabyAHCVB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Palacios-BejaranoGRG13,
author = {Bernardo Palacios{-}Bejarano and
Gonzalo Cerruela Garc{\'{\i}}a and
Irene Luque Ruiz and
Miguel {\'{A}}ngel G{\'{o}}mez{-}Nieto},
title = {{QSAR} model based on weighted {MCS} trees approach for the representation
of molecule data sets},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {2},
pages = {185--201},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9637-7},
doi = {10.1007/S10822-013-9637-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Palacios-BejaranoGRG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PangCLJZRAZ13,
author = {Chunli Pang and
Tianguang Cao and
Junwei Li and
Mengwen Jia and
Suhua Zhang and
Shuxi Ren and
Hailong An and
Yong Zhan},
title = {Combining fragment homology modeling with molecular dynamics aims
at prediction of Ca\({}^{\mbox{2+}}\) binding sites in CaBPs},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {8},
pages = {697--705},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9668-0},
doi = {10.1007/S10822-013-9668-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PangCLJZRAZ13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PerdihWS13,
author = {Andrej Perdih and
Gerhard Wolber and
Tomaz Solmajer},
title = {Molecular dynamics simulation and linear interaction energy study
of d-Glu-based inhibitors of the MurD ligase},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {8},
pages = {723--738},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9673-3},
doi = {10.1007/S10822-013-9673-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PerdihWS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PerezAGDGGT13,
author = {Bianca P{\'{e}}rez and
Sandra Antunes and
L{\'{\i}}dia M. Gon{\c{c}}alves and
Ana Domingos and
Jos{\'{e}} R. B. Gomes and
Paula Gomes and
C{\'{a}}tia Teixeira},
title = {Toward the discovery of inhibitors of babesipain-1, a Babesia bigemina
cysteine protease: in vitro evaluation, homology modeling and molecular
docking studies},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {9},
pages = {823--835},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9682-2},
doi = {10.1007/S10822-013-9682-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PerezAGDGGT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PolishchukMV13,
author = {Pavel G. Polishchuk and
Timur I. Madzhidov and
Alexandre Varnek},
title = {Estimation of the size of drug-like chemical space based on {GDB-17}
data},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {8},
pages = {675--679},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9672-4},
doi = {10.1007/S10822-013-9672-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PolishchukMV13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/PrajapatiSPKBBS13,
author = {Rameshwar Prajapati and
Udghosh Singh and
Abhijeet Patil and
Kailas S. Khomane and
Pravin Bagul and
Arvind K. Bansal and
Abhay T. Sangamwar},
title = {In silico model for P-glycoprotein substrate prediction: insights
from molecular dynamics and in vitro studies},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {4},
pages = {347--363},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9650-x},
doi = {10.1007/S10822-013-9650-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/PrajapatiSPKBBS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/RuusmannM13,
author = {Villu Ruusmann and
Uko Maran},
title = {From data point timelines to a well curated data set, data mining
of experimental data and chemical structure data from scientific articles,
problems and possible solutions},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {7},
pages = {583--603},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9664-4},
doi = {10.1007/S10822-013-9664-4},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/RuusmannM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SaikiaD13,
author = {Nabanita Saikia and
Ramesh C. Deka},
title = {Ab initio study on the noncovalent adsorption of camptothecin anticancer
drug onto graphene, defect modified graphene and graphene oxide},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {9},
pages = {807--821},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9681-3},
doi = {10.1007/S10822-013-9681-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SaikiaD13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SaikiaRD13,
author = {Nabanita Saikia and
Sanchaita Rajkhowa and
Ramesh C. Deka},
title = {Density functional and molecular docking studies towards investigating
the role of single-wall carbon nanotubes as nanocarrier for loading
and delivery of pyrazinamide antitubercular drug onto pncA protein},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {3},
pages = {257--276},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9638-6},
doi = {10.1007/S10822-013-9638-6},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SaikiaRD13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SalminaGP13,
author = {Elena Salmina and
Maria A. Grishina and
Vladimir Potemkin},
title = {An approximation of the Cioslowski-Mixon bond order indexes using
the AlteQ approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {9},
pages = {793--805},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9677-z},
doi = {10.1007/S10822-013-9677-Z},
timestamp = {Wed, 12 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SalminaGP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SastryADAS13,
author = {G. Madhavi Sastry and
Matvey Adzhigirey and
Tyler Day and
Ramakrishna Annabhimoju and
Woody Sherman},
title = {Protein and ligand preparation: parameters, protocols, and influence
on virtual screening enrichments},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {3},
pages = {221--234},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9644-8},
doi = {10.1007/S10822-013-9644-8},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/SastryADAS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/SchneiderLHKR13,
author = {Nadine Schneider and
Gudrun Lange and
Sally A. Hindle and
Robert Klein and
Matthias Rarey},
title = {A consistent description of HYdrogen bond and DEhydration energies
in protein-ligand complexes: methods behind the {HYDE} scoring function},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {1},
pages = {15--29},
year = {2013},
url = {https://doi.org/10.1007/s10822-012-9626-2},
doi = {10.1007/S10822-012-9626-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SchneiderLHKR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TanMCLPSY13,
author = {Wen Tan and
Hu Mei and
Li Chao and
Tengfei Liu and
Xianchao Pan and
Mao Shu and
Li Yang},
title = {Combined {QSAR} and molecule docking studies on predicting P-glycoprotein
inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {12},
pages = {1067--1073},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9697-8},
doi = {10.1007/S10822-013-9697-8},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TanMCLPSY13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TitarenkoVZKG13,
author = {Zoya Titarenko and
Natalya Vasilevich and
Vladimir Zernov and
Michael Kirpichenok and
Dmitry Genis},
title = {Oxygen-containing fragments in natural products},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {2},
pages = {125--160},
year = {2013},
url = {https://doi.org/10.1007/s10822-012-9629-z},
doi = {10.1007/S10822-012-9629-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TitarenkoVZKG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TothBH13,
author = {Gergely T{\'{o}}th and
Zsolt Bodai and
K{\'{a}}roly H{\'{e}}berger},
title = {Estimation of influential points in any data set from coefficient
of determination and its leave-one-out cross-validated counterpart},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {10},
pages = {837--844},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9680-4},
doi = {10.1007/S10822-013-9680-4},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TothBH13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TranLT13,
author = {Diem{-}Trang T. Tran and
Ly Le and
Thanh N. Truong},
title = {Discover binding pathways using the sliding binding-box docking approach:
application to binding pathways of oseltamivir to avian influenza
{H5N1} neuraminidase},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {8},
pages = {689--695},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9675-1},
doi = {10.1007/S10822-013-9675-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TranLT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TsengMBS13,
author = {Yufeng Jane Tseng and
Eric J. Martin and
Cristian Bologa and
Anang A. Shelat},
title = {Cheminformatics aspects of high throughput screening: from robots
to models: symposium summary},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {5},
pages = {443--453},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9646-6},
doi = {10.1007/S10822-013-9646-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TsengMBS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VarelaCSJ13,
author = {Rocco Varela and
Ann E. Cleves and
Russell Spitzer and
Ajay N. Jain},
title = {A structure-guided approach for protein pocket modeling and affinity
prediction},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {11},
pages = {917--934},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9688-9},
doi = {10.1007/S10822-013-9688-9},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/VarelaCSJ13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WangCYS13,
author = {Kai Wang and
John D. Chodera and
Yanzhi Yang and
Michael R. Shirts},
title = {Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian
replica exchange molecular dynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {12},
pages = {989--1007},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9689-8},
doi = {10.1007/S10822-013-9689-8},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WangCYS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WangSPSAHNP13,
author = {Hao Wang and
Richard B. Sessions and
Stephen S. Prime and
Deborah K. Shoemark and
Shelley J. Allen and
Wei Hong and
Sathya Narayanan and
Ian C. Paterson},
title = {Identification of novel small molecule TGF-{\(\beta\)} antagonists
using structure-based drug design},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {4},
pages = {365--372},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9651-9},
doi = {10.1007/S10822-013-9651-9},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WangSPSAHNP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WirthVZRMRS13,
author = {Matthias Wirth and
Andrea Volkamer and
Vincent Zoete and
Friedrich Rippmann and
Olivier Michielin and
Matthias Rarey and
Wolfgang H. B. Sauer},
title = {Protein pocket and ligand shape comparison and its application in
virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {6},
pages = {511--524},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9659-1},
doi = {10.1007/S10822-013-9659-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WirthVZRMRS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WoodCENS13,
author = {David J. Wood and
Lars Carlsson and
Martin Eklund and
Ulf Norinder and
Jonna C. St{\aa}lring},
title = {{QSAR} with experimental and predictive distributions: an information
theoretic approach for assessing model quality},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {3},
pages = {203--219},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9639-5},
doi = {10.1007/S10822-013-9639-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WoodCENS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/WrightASDK13,
author = {James S. Wright and
James M. Anderson and
Hooman Shadnia and
Tony Durst and
John A. Katzenellenbogen},
title = {Experimental versus predicted affinities for ligand binding to estrogen
receptor: iterative selection and rescoring of docked poses systematically
improves the correlation},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {8},
pages = {707--721},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9670-6},
doi = {10.1007/S10822-013-9670-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/WrightASDK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YangYZ13,
author = {Zhiwei Yang and
Gang Yang and
Lijun Zhou},
title = {Mutation effects of neuraminidases and their docking with ligands:
a molecular dynamics and free energy calculation study},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {11},
pages = {935--950},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9691-1},
doi = {10.1007/S10822-013-9691-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YangYZ13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YuanTHLZYRLKXXCL13,
author = {Haoliang Yuan and
Wenting Tai and
Shihe Hu and
Haichun Liu and
Yanmin Zhang and
Sihui Yao and
Ting Ran and
Shuai Lu and
Zhipeng Ke and
Xiao Xiong and
Jinxing Xu and
Yadong Chen and
Tao Lu},
title = {Fragment-based strategy for structural optimization in combination
with 3D-QSAR},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {10},
pages = {897--915},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9687-x},
doi = {10.1007/S10822-013-9687-X},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/YuanTHLZYRLKXXCL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZanuySRBAKJCNSSRA13,
author = {David Zanuy and
Francisco J. Sayago and
Guillem Revilla{-}L{\'{o}}pez and
Gema Ballano and
Lilach Agemy and
Venkata Ramana Kotamraju and
Ana I. Jim{\'{e}}nez and
Carlos Cativiela and
Ruth Nussinov and
April M. Sawvel and
Galen Stucky and
Erkki Ruoslahti and
Carlos Alem{\'{a}}n},
title = {Engineering strategy to improve peptide analogs: from structure-based
computational design to tumor homing},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {1},
pages = {31--43},
year = {2013},
url = {https://doi.org/10.1007/s10822-012-9623-5},
doi = {10.1007/S10822-012-9623-5},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/ZanuySRBAKJCNSSRA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZauharGW13,
author = {Randy J. Zauhar and
Eleonora Gianti and
William J. Welsh},
title = {Fragment-based Shape Signatures: a new tool for virtual screening
and drug discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {12},
pages = {1009--1036},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9698-7},
doi = {10.1007/S10822-013-9698-7},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZauharGW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhangZZPJZT13,
author = {Wenshuai Zhang and
Xiaoyan Zeng and
Li Zhang and
Haiyan Peng and
Yongjun Jiao and
Jun Zeng and
Herbert R. Treutlein},
title = {Computational identification of epitopes in the glycoproteins of novel
bunyavirus {(SFTS} virus) recognized by a human monoclonal antibody
(MAb 4-5)},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {6},
pages = {539--550},
year = {2013},
url = {https://doi.org/10.1007/s10822-013-9661-7},
doi = {10.1007/S10822-013-9661-7},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZhangZZPJZT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhouWTRYH13,
author = {Peng Zhou and
Congcong Wang and
Feifei Tian and
Yanrong Ren and
Chao Yang and
Jian Huang},
title = {Biomacromolecular quantitative structure-activity relationship (BioQSAR):
a proof-of-concept study on the modeling, prediction and interpretation
of protein-protein binding affinity},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {1},
pages = {67--78},
year = {2013},
url = {https://doi.org/10.1007/s10822-012-9625-3},
doi = {10.1007/S10822-012-9625-3},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZhouWTRYH13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ZhuLLKYJGCZJLL13,
author = {Kongkai Zhu and
Junyan Lu and
Zhongjie Liang and
Xiangqian Kong and
Fei Ye and
Lu Jin and
Heji Geng and
Yong Chen and
Mingyue Zheng and
Hualiang Jiang and
Jun{-}Qian Li and
Cheng Luo},
title = {A quantum mechanics/molecular mechanics study on the hydrolysis mechanism
of New Delhi metallo-{\(\beta\)}-lactamase-1},
journal = {J. Comput. Aided Mol. Des.},
volume = {27},
number = {3},
pages = {247--256},
year = {2013},
url = {https://doi.org/10.1007/s10822-012-9630-6},
doi = {10.1007/S10822-012-9630-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ZhuLLKYJGCZJLL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Abagyan12,
author = {Ruben Abagyan},
title = {Computational chemistry in 25 years},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {9--10},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9516-z},
doi = {10.1007/S10822-011-9516-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Abagyan12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AbdoCLJP12,
author = {Ammar Abdo and
S{\'{e}}gol{\`{e}}ne Caboche and
Val{\'{e}}rie Lecl{\`{e}}re and
Philippe Jacques and
Maude Pupin},
title = {A new fingerprint to predict nonribosomal peptides activity},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {10},
pages = {1187--1194},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9608-4},
doi = {10.1007/S10822-012-9608-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AbdoCLJP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AbdoSHAS12,
author = {Ammar Abdo and
Faisal Saeed and
Hamza Hentabli and
Ali Ahmed and
Naomie Salim},
title = {Ligand expansion in ligand-based virtual screening using relevance
feedback},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {3},
pages = {279--287},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9543-4},
doi = {10.1007/S10822-012-9543-4},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AbdoSHAS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AlvaradoJD12,
author = {Omar Alvarado and
Gonzalo A. Ja{\~{n}}a and
Eduardo J. Delgado},
title = {Computer-assisted study on the reaction between pyruvate and ylide
in the pathway leading to lactyl-ThDP},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {8},
pages = {977--982},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9589-3},
doi = {10.1007/S10822-012-9589-3},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AlvaradoJD12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AndreCATCM12,
author = {Joseph R. Andr{\'{e}} and
Marie{-}Jeanne Cl{\'{e}}ment and
Elisabeth Adjadj and
Flavio Toma and
Patrick A. Curmi and
Philippe Manivet},
title = {The state of the guanosine nucleotide allosterically affects the interfaces
of tubulin in protofilament},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {4},
pages = {397--407},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9566-x},
doi = {10.1007/S10822-012-9566-X},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/AndreCATCM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/AnnapooraniUPPR12,
author = {Angusamy Annapoorani and
Venugopal Umamageswaran and
Radhakrishnan Parameswari and
Shunmugiah Karutha Pandian and
Arumugam Veera Ravi},
title = {Computational discovery of putative quorum sensing inhibitors against
LasR and RhlR receptor proteins of Pseudomonas aeruginosa},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {9},
pages = {1067--1077},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9599-1},
doi = {10.1007/S10822-012-9599-1},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/AnnapooraniUPPR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Bajorath12,
author = {J{\"{u}}rgen Bajorath},
title = {Computational chemistry in pharmaceutical research: at the crossroads},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {11--12},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9488-z},
doi = {10.1007/S10822-011-9488-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Bajorath12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BallanteMMR12,
author = {Flavio Ballante and
Ira Musmuca and
Garland R. Marshall and
Rino Ragno},
title = {Comprehensive model of wild-type and mutant {HIV-1} reverse transciptases},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {8},
pages = {907--919},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9586-6},
doi = {10.1007/S10822-012-9586-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BallanteMMR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BarbosaPF12,
author = {Euz{\'{e}}bio G. Barbosa and
Kerly F. M. Pasqualoto and
M{\'{a}}rcia M. C. Ferreira},
title = {The receptor-dependent {LQTA-QSAR:} application to a set of trypanothione
reductase inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {9},
pages = {1055--1065},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9598-2},
doi = {10.1007/S10822-012-9598-2},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BarbosaPF12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BarrilL12,
author = {Xavier Barril and
F. Javier Luque},
title = {Molecular simulation methods in drug discovery: a prospective outlook},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {81--86},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9506-1},
doi = {10.1007/S10822-011-9506-1},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BarrilL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BasuS12,
author = {Arijit Basu and
Barij N. Sinha},
title = {Understanding the molecular interactions of different radical scavengers
with ribonucleotide reductase {M2} (hRRM2) domain: opening the gates
and gaining access},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {7},
pages = {865--881},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9581-y},
doi = {10.1007/S10822-012-9581-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BasuS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BecksteinI12,
author = {Oliver Beckstein and
Bogdan I. Iorga},
title = {Prediction of hydration free energies for aliphatic and aromatic chloro
derivatives using molecular dynamics simulations with the {OPLS-AA}
force field},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {5},
pages = {635--645},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9527-9},
doi = {10.1007/S10822-011-9527-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BecksteinI12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BensonFUDZM12,
author = {Mark L. Benson and
John C. Faver and
Melek N. Ucisik and
Danial S. Dashti and
Zheng Zheng and
Kenneth M. Merz Jr.},
title = {Prediction of trypsin/molecular fragment binding affinities by free
energy decomposition and empirical scores},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {5},
pages = {647--659},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9567-9},
doi = {10.1007/S10822-012-9567-9},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BensonFUDZM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Blaney12,
author = {Jeff Blaney},
title = {A very short history of structure-based design: how did we get here
and where do we need to go?},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {13--14},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9518-x},
doi = {10.1007/S10822-011-9518-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Blaney12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BorhaniS12,
author = {David W. Borhani and
David E. Shaw},
title = {The future of molecular dynamics simulations in drug discovery},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {15--26},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9517-y},
doi = {10.1007/S10822-011-9517-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BorhaniS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Brown12,
author = {Frank K. Brown},
title = {Democratization of computational chemistry and Chem(o)informatics},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {27--28},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9491-4},
doi = {10.1007/S10822-011-9491-4},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Brown12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BrozellMBRCR12,
author = {Scott R. Brozell and
Sudipto Mukherjee and
Trent E. Balius and
Daniel R. Roe and
David A. Case and
Robert C. Rizzo},
title = {Evaluation of {DOCK} 6 as a pose generation and database enrichment
tool},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {6},
pages = {749--773},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9565-y},
doi = {10.1007/S10822-012-9565-Y},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BrozellMBRCR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CabreraGM12,
author = {{\'{A}}lvaro Cort{\'{e}}s Cabrera and
Federico Gago and
Antonio Morreale},
title = {A reverse combination of structure-based and ligand-based strategies
for virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {3},
pages = {319--327},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9558-x},
doi = {10.1007/S10822-012-9558-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CabreraGM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CabreraMGA12,
author = {{\'{A}}lvaro Cort{\'{e}}s Cabrera and
Antonio Morreale and
Federico Gago and
Celerino Abad{-}Zapatero},
title = {AtlasCBS: a web server to map and explore chemico-biological space},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {9},
pages = {995--1003},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9587-5},
doi = {10.1007/S10822-012-9587-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CabreraMGA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ChaubeyDO12,
author = {Amit Kumar Chaubey and
Kshatresh Dutta Dubey and
Rajendra Prasad Ojha},
title = {Stability and free energy calculation of {LNA} modified quadruplex:
a molecular dynamics study},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {3},
pages = {289--299},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9548-z},
doi = {10.1007/S10822-012-9548-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ChaubeyDO12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ClarkW12,
author = {Robert D. Clark and
Marvin Waldman},
title = {Lions and tigers and bears, oh my! Three barriers to progress in computer-aided
molecular design},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {29--34},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9504-3},
doi = {10.1007/S10822-011-9504-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ClarkW12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/CorbeilWL12,
author = {Christopher R. Corbeil and
Christopher I. Williams and
Paul Labute},
title = {Variability in docking success rates due to dataset preparation},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {6},
pages = {775--786},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9570-1},
doi = {10.1007/S10822-012-9570-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/CorbeilWL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Cramer12,
author = {Richard D. Cramer},
title = {The inevitable {QSAR} renaissance},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {35--38},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9495-0},
doi = {10.1007/S10822-011-9495-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Cramer12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Cramer12a,
author = {Richard D. Cramer},
title = {R-group template CoMFA combines benefits of "ad hoc" and topomer alignments
using 3D-QSAR for lead optimization},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {7},
pages = {805--819},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9583-9},
doi = {10.1007/S10822-012-9583-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Cramer12a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DegreveFC12,
author = {L{\'{e}}o Degr{\`{e}}ve and
Carlos A. Fuzo and
Antonio Caliri},
title = {Extensive structural change of the envelope protein of dengue virus
induced by a tuned ionic strength: conformational and energetic analyses},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {12},
pages = {1311--1325},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9616-4},
doi = {10.1007/S10822-012-9616-4},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/DegreveFC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DunkernPKGRBAM12,
author = {Torsten Dunkern and
Arati Prabhu and
Prashant Suresh Kharkar and
Heike Goebel and
Edith Rolser and
Waltraud Burckhard{-}Boer and
Premkumar Arumugam and
Mahindra T. Makhija},
title = {Virtual and experimental high-throughput screening {(HTS)} in search
of novel inosine 5{\({'}\)}-monophosphate dehydrogenase {II}
{(IMPDH} {II)} inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {11},
pages = {1277--1292},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9615-5},
doi = {10.1007/S10822-012-9615-5},
timestamp = {Tue, 12 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DunkernPKGRBAM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ErtlL12,
author = {Peter Ertl and
Richard Lewis},
title = {{IADE:} a system for intelligent automatic design of bioisosteric
analogs},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {11},
pages = {1207--1215},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9609-3},
doi = {10.1007/S10822-012-9609-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ErtlL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Gago12,
author = {Federico Gago},
title = {Reflections on the past 25 years},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {45},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9510-5},
doi = {10.1007/S10822-011-9510-5},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Gago12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GallandKQ12,
author = {Nicolas Galland and
Soleymane Kone and
Jean{-}Yves Le Questel},
title = {Mapping of the interaction sites of galanthamine: a quantitative analysis
through pairwise potentials and quantum chemistry},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {10},
pages = {1111--1126},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9602-x},
doi = {10.1007/S10822-012-9602-X},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GallandKQ12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GallicchioL12,
author = {Emilio Gallicchio and
Ronald M. Levy},
title = {Prediction of {SAMPL3} host-guest affinities with the binding energy
distribution analysis method {(BEDAM)}},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {5},
pages = {505--516},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9552-3},
doi = {10.1007/S10822-012-9552-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GallicchioL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GeballeG12,
author = {Matthew T. Geballe and
J. Peter Guthrie},
title = {The {SAMPL3} blind prediction challenge: transfer energy overview},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {5},
pages = {489--496},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9568-8},
doi = {10.1007/S10822-012-9568-8},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GeballeG12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GengGCTJC12,
author = {Lingling Geng and
Jian Gao and
Wei Cui and
Yancheng Tang and
Mingjuan Ji and
Bozhen Chen},
title = {Computational insights into the selectivity mechanism of {APP-IP}
over matrix metalloproteinases},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {12},
pages = {1327--1342},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9617-3},
doi = {10.1007/S10822-012-9617-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GengGCTJC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Glen12,
author = {Robert C. Glen},
title = {Computational chemistry and cheminformatics: an essay on the future},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {47--49},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9501-6},
doi = {10.1007/S10822-011-9501-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Glen12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GraziosoLTEMM12,
author = {Giovanni Grazioso and
Laura Legnani and
Lucio Toma and
Roberta Ettari and
Nicola Micale and
Carlo De Micheli},
title = {Mechanism of falcipain-2 inhibition by {\(\alpha\)}, {\(\beta\)}-unsaturated
benzo[1, 4]diazepin-2-one methyl ester},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {9},
pages = {1035--1043},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9596-4},
doi = {10.1007/S10822-012-9596-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GraziosoLTEMM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GreenLH12,
author = {Darren V. S. Green and
Andrew R. Leach and
Martha S. Head},
title = {Computer-aided molecular design under the SWOTlight},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {51--56},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9514-1},
doi = {10.1007/S10822-011-9514-1},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/GreenLH12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HamaguchiFW12,
author = {Nobuko Hamaguchi and
Laszlo Fusti{-}Molnar and
Stanislaw Wlodek},
title = {Force-field and quantum-mechanical binding study of selected {SAMPL3}
host-guest complexes},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {5},
pages = {577--582},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9553-2},
doi = {10.1007/S10822-012-9553-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HamaguchiFW12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HechtF12,
author = {David Hecht and
Gary B. Fogel},
title = {Modeling the evolution of drug resistance in malaria},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {12},
pages = {1343--1353},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9618-2},
doi = {10.1007/S10822-012-9618-2},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HechtF12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HeimL12,
author = {Andrew J. Heim and
Zhijun Li},
title = {Developing a high-quality scoring function for membrane protein structures
based on specific inter-residue interactions},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {3},
pages = {301--309},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9556-z},
doi = {10.1007/S10822-012-9556-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HeimL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HouCTLLGH12,
author = {Jin{-}Qiang Hou and
Shuo{-}Bin Chen and
Jia{-}Heng Tan and
Hai{-}Bin Luo and
Ding Li and
Lian{-}Quan Gu and
Zhi{-}Shu Huang},
title = {New insights from molecular dynamic simulation studies of the multiple
binding modes of a ligand with G-quadruplex {DNA}},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {12},
pages = {1355--1368},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9619-1},
doi = {10.1007/S10822-012-9619-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HouCTLLGH12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HuangC12,
author = {Y.{-}H. Huang and
Chi{-}Ming Chen},
title = {Statistical analyses and computational prediction of helical kinks
in membrane proteins},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {10},
pages = {1171--1185},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9607-5},
doi = {10.1007/S10822-012-9607-5},
timestamp = {Fri, 28 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/HuangC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/HuangG12,
author = {Liang{-}Tsung Huang and
M. Michael Gromiha},
title = {Real value prediction of protein folding rate change upon point mutation},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {3},
pages = {339--347},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9560-3},
doi = {10.1007/S10822-012-9560-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/HuangG12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JainC12,
author = {Ajay N. Jain and
Ann E. Cleves},
title = {Does your model weigh the same as a Duck?},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {57--67},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9530-1},
doi = {10.1007/S10822-011-9530-1},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/JainC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JohnstonFN12,
author = {Michael A. Johnston and
Damien Farrell and
Jens Erik Nielsen},
title = {A collaborative environment for developing and validating predictive
tools for protein biophysical characteristics},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {4},
pages = {387--396},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9564-z},
doi = {10.1007/S10822-012-9564-Z},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/JohnstonFN12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/JungLKCKPCCJ12,
author = {Eunkyoung Jung and
Nam{-}Kyung Lee and
Sang{-}Kee Kang and
Seung{-}Hoon Choi and
Daejin Kim and
Kisoo Park and
Kihang Choi and
Yun{-}Jaie Choi and
Dong Hyun Jung},
title = {Identification of tissue-specific targeting peptide},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {11},
pages = {1267--1275},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9614-6},
doi = {10.1007/S10822-012-9614-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/JungLKCKPCCJ12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KalidWSSS12,
author = {Ori Kalid and
Dora Toledo Warshaviak and
Sharon Shechter and
Woody Sherman and
Sharon Shacham},
title = {Consensus Induced Fit Docking (cIFD): methodology, validation, and
application to the discovery of novel Crm1 inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {11},
pages = {1217--1228},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9611-9},
doi = {10.1007/S10822-012-9611-9},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KalidWSSS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KarK12,
author = {Parimal Kar and
Volker Knecht},
title = {Energetic basis for drug resistance of {HIV-1} protease mutants against
amprenavir},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {2},
pages = {215--232},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9550-5},
doi = {10.1007/S10822-012-9550-5},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KarK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KawatkarMMJ12,
author = {Sameer Kawatkar and
Demetri Moustakas and
Matthew Miller and
Diane Joseph{-}McCarthy},
title = {Virtual fragment screening: exploration of {MM-PBSA} re-scoring},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {8},
pages = {921--934},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9590-x},
doi = {10.1007/S10822-012-9590-X},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KawatkarMMJ12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KehoeFD12,
author = {Charles W. Kehoe and
Christopher J. Fennell and
Ken A. Dill},
title = {Testing the semi-explicit assembly solvation model in the {SAMPL3}
community blind test},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {5},
pages = {563--568},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9536-8},
doi = {10.1007/S10822-011-9536-8},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KehoeFD12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Kenny12,
author = {Peter W. Kenny},
title = {Computation, experiment and molecular design},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {69--72},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9515-0},
doi = {10.1007/S10822-011-9515-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Kenny12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KonigB12,
author = {Gerhard K{\"{o}}nig and
Bernard R. Brooks},
title = {Predicting binding affinities of host-guest systems in the {SAMPL3}
blind challenge: the performance of relative free energy calculations},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {5},
pages = {543--550},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9525-y},
doi = {10.1007/S10822-011-9525-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KonigB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KorbBRKE12,
author = {Oliver Korb and
Tim ten Brink and
Fredrick Robin Devadoss and
Victor Paul Raj and
Matthias Keil and
Thomas E. Exner},
title = {Are predefined decoy sets of ligand poses able to quantify scoring
function accuracy?},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {2},
pages = {185--197},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9539-5},
doi = {10.1007/S10822-011-9539-5},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KorbBRKE12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KulpBWBG12,
author = {John L. Kulp III and
Seth N. Blumenthal and
Qiang Wang and
Richard L. Bryan and
Frank Guarnieri},
title = {A fragment-based approach to the {SAMPL3} Challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {5},
pages = {583--594},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9546-1},
doi = {10.1007/S10822-012-9546-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KulpBWBG12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KumarZ12,
author = {Ashutosh Kumar and
Kam Y. J. Zhang},
title = {Computational fragment-based screening using RosettaLigand: the {SAMPL3}
challenge},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {5},
pages = {603--616},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9523-0},
doi = {10.1007/S10822-011-9523-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/KumarZ12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Kuntz12,
author = {Irwin D. Kuntz},
title = {Darwinian Docking},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {73--75},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9503-4},
doi = {10.1007/S10822-011-9503-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Kuntz12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LawrenzWONM12,
author = {Morgan Lawrenz and
Jeff Wereszczynski and
Juan Manuel Ortiz{-}S{\'{a}}nchez and
Sara E. Nichols and
James Andrew McCammon},
title = {Thermodynamic integration to predict host-guest binding affinities},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {5},
pages = {569--576},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9542-5},
doi = {10.1007/S10822-012-9542-5},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LawrenzWONM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiB12,
author = {Ruifang Li and
J{\"{u}}rgen Bajorath},
title = {Systematic assessment of scaffold distances in ChEMBL: prioritization
of compound data sets for scaffold hopping analysis in virtual screening},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {10},
pages = {1101--1109},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9603-9},
doi = {10.1007/S10822-012-9603-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiebeschuetzCK12,
author = {John W. Liebeschuetz and
Jason C. Cole and
Oliver Korb},
title = {Pose prediction and virtual screening performance of {GOLD} scoring
functions in a standardized test},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {6},
pages = {737--748},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9551-4},
doi = {10.1007/S10822-012-9551-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiebeschuetzCK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiebeschuetzHOG12,
author = {John W. Liebeschuetz and
Jana Hennemann and
Tjelvar S. G. Olsson and
Colin R. Groom},
title = {The good, the bad and the twisted: a survey of ligand geometry in
protein crystal structures},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {2},
pages = {169--183},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9538-6},
doi = {10.1007/S10822-011-9538-6},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiebeschuetzHOG12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LiiH12,
author = {Jenn{-}Huei Lii and
Ching{-}Han Hu},
title = {An improved theoretical approach to the empirical corrections of density
functional theory},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {2},
pages = {199--213},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9534-x},
doi = {10.1007/S10822-011-9534-X},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LiiH12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LinderJOLB12,
author = {Mats Linder and
Adam Johannes Johansson and
Tjelvar S. G. Olsson and
John W. Liebeschuetz and
Tore Brinck},
title = {Computational design of a Diels-Alderase from a thermophilic esterase:
the importance of dynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {9},
pages = {1079--1095},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9601-y},
doi = {10.1007/S10822-012-9601-Y},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LinderJOLB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LokwaniSMSS12,
author = {Deepak Lokwani and
Reecha Shah and
Santosh Mokale and
Padma Shastry and
Devanand Shinde},
title = {Development of energetic pharmacophore for the designing of 1, 2,
3, 4-tetrahydropyrimidine derivatives as selective cyclooxygenase-2
inhibitors},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {3},
pages = {267--277},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9540-z},
doi = {10.1007/S10822-011-9540-Z},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LokwaniSMSS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LupyanAS12,
author = {Dmitry Lupyan and
Yuriy A. Abramov and
Woody Sherman},
title = {Close intramolecular sulfur-oxygen contacts: modified force field
parameters for improved conformation generation},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {11},
pages = {1195--1205},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9610-x},
doi = {10.1007/S10822-012-9610-X},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LupyanAS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Maggiora12,
author = {Gerald M. Maggiora},
title = {Is there a future for computational chemistry in drug research?},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {87--90},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9493-2},
doi = {10.1007/S10822-011-9493-2},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Maggiora12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Marrero-PonceSLBT12,
author = {Yovani Marrero{-}Ponce and
Oscar Mart{\'{\i}}nez Santiago and
Yoan Mart{\'{\i}}nez L{\'{o}}pez and
Stephen J. Barigye and
Francisco Torrens},
title = {Derivatives in discrete mathematics: a novel graph-theoretical invariant
for generating new 2/3D molecular descriptors. I. Theory and {QSPR}
application},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {11},
pages = {1229--1246},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9591-9},
doi = {10.1007/S10822-012-9591-9},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/Marrero-PonceSLBT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Marshall12,
author = {Garland R. Marshall},
title = {Limiting assumptions in structure-based design: binding entropy},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {3--8},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9494-1},
doi = {10.1007/S10822-011-9494-1},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Marshall12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/MartinEHDL12,
author = {Eric J. Martin and
Peter Ertl and
Peter Hunt and
Jos{\'{e}} S. Duca and
Richard Lewis},
title = {Gazing into the crystal ball; the future of computer-aided drug design},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {77--79},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9487-0},
doi = {10.1007/S10822-011-9487-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/MartinEHDL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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