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Journal of Computer-Aided Molecular Design, Volume 34
Volume 34, Number 1, January 2020
- Filip Miljkovic
, Jürgen Bajorath
:
Data structures for computational compound promiscuity analysis and exemplary applications to inhibitors of the human kinome. 1-10 - Xiaoqian Xu
, Li Zhang, Ying Cai, Dongxin Liu, Zhengwen Shang, Qiuhong Ren, Qiong Li, Weidong Zhao, Yuhua Chen:
Inhibitor discovery for the E. coli meningitis virulence factor IbeA from homology modeling and virtual screening. 11-25 - Chonnikan Hanpaibool, Matina Leelawiwat, Kaito Takahashi
, Thanyada Rungrotmongkol:
Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase. 27-37 - Radhika Vangala, Sree Kanth Sivan
, Saikiran Reddy Peddi, Vijjulatha Manga
:
Computational design, synthesis and evaluation of new sulphonamide derivatives targeting HIV-1 gp120. 39-54 - Maxim Gureev, Daria Novikova
, Tatyana Grigoreva
, Svetlana Vorona
, Alexander Garabadzhiu, Vyacheslav Tribulovich
:
Simulation of MDM2 N-terminal domain conformational lability in the presence of imidazoline based inhibitors of MDM2-p53 protein-protein interaction. 55-70 - Andreas Mecklenfeld
, Gabriele Raabe
:
Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energies. 71-82 - Lakshmi Maganti, Dhananjay Bhattacharyya
:
Sequence specificity in DNA-drug intercalation: MD simulation and density functional theory approaches. 83-95
Volume 34, Number 2, February 2020
- Michael K. Gilson, Rommie E. Amaro
:
Drug Design Data Resource, Grand Challenge 4, second of two issues. 97 - Conor D. Parks, Zied Gaieb, Michael Chiu, Huanwang Yang, Chenghua Shao
, W. Patrick Walters, Johanna M. Jansen, Georgia B. McGaughey, Richard A. Lewis, Scott D. Bembenek, Michael K. Ameriks, Tara Mirzadegan, Stephen K. Burley, Rommie E. Amaro
, Michael K. Gilson
:
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. 99-119 - Oleg V. Stroganov
, Fedor N. Novikov, Michael G. Medvedev
, Artem O. Dmitrienko
, Igor S. Gerasimov
, Igor V. Svitanko, Ghermes G. Chilov:
The role of human in the loop: lessons from D3R challenge 4. 121-130 - Duc Duy Nguyen
, Kaifu Gao, Menglun Wang, Guo-Wei Wei
:
MathDL: mathematical deep learning for D3R Grand Challenge 4. 131-147 - Andrea Basciu
, Panagiotis I. Koukos, Giuliano Malloci
, Alexandre M. J. J. Bonvin
, Attilio Vittorio Vargiu
:
Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. 149-162 - Sukanya Sasmal
, Lea El-Khoury, David L. Mobley
:
D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors. 163-177 - Sergei Kotelnikov, Andrey Alekseenko
, Cong Liu
, Mikhail Ignatov, Dzmitry Padhorny, Emiliano Brini, Mark Lukin, Evangelos A. Coutsias, Ken A. Dill, Dima Kozakov
:
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4. 179-189 - Maria Kadukova
, Vladimir Chupin, Sergei Grudinin
:
Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4. 191-200 - Bo Wang, Ho-Leung Ng
:
Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4. 201-217
Volume 34, Number 3, March 2020
- George Nicola
, Irina Kufareva
, Andrey V. Ilatovskiy, Ruben Abagyan
:
Druggable exosites of the human kino-pocketome. 219-230 - Gustav Olanders
, Hiba Alogheli, Peter Brandt
, Anders Karlén
:
Conformational analysis of macrocycles: comparing general and specialized methods. 231-252 - Alberto Mills
, Federico Gago
:
Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts. 253-265 - Jesús Sánchez-Márquez
, Victor García, David Zorrilla
, Manuel Fernández:
Software to obtain spatially localized functions from different radial functions. 267-280 - Gennady I. Makarov
, T. M. Makarova:
A noncanonical binding site of linezolid revealed via molecular dynamics simulations. 281-291 - Martiniano Bello
, Concepción Guadarrama-García, Rolando Alberto Rodriguez-Fonseca
:
Dissecting the molecular recognition of dual lapatinib derivatives for EGFR/HER2. 293-303 - Gonzalo Cerruela García
, José Pérez-Parras Toledano, Aida de Haro-García, Nicolás García-Pedrajas:
Influence of feature rankers in the construction of molecular activity prediction models. 305-325
Volume 34, Number 4, April 2020
- Maximiliano Riquelme, Esteban Vöhringer-Martinez
:
SAMPL6 Octanol-water partition coefficients from alchemical free energy calculations with MBIS atomic charges. 327-334 - Mehtap Isik
, Teresa Danielle Bergazin
, Thomas Fox
, Andrea Rizzi
, John D. Chodera
, David L. Mobley
:
Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. 335-370 - Piero Procacci
, Guido Guarnieri
:
SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches. 371-384 - Christoph Loschen
, Jens Reinisch, Andreas Klamt:
COSMO-RS based predictions for the SAMPL6 logP challenge. 385-392 - Shuzhe Wang
, Sereina Riniker
:
Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge. 393-403 - Mehtap Isik
, Dorothy Levorse, David L. Mobley
, Timothy Rhodes
, John D. Chodera
:
Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. 405-420 - Ye Ding
, You Xu, Cheng Qian, Jinfeng Chen, Jian Zhu, Houhou Huang, Yi Shi
, Jing Huang
:
Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields. 421-435 - Alexei M. Nikitin
:
Non-zero Lennard-Jones parameters for the Toukan-Rahman water model: more accurate calculations of the solvation free energy of organic substances. 437-441 - William J. Zamora
, Silvana Pinheiro, Kilian German, Clara Pérez-Ràfols, Carles Curutchet
, F. Javier Luque
:
Prediction of the n-octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations. 443-451 - Nicolas Tielker, Daniel Tomazic, Lukas Eberlein, Stefan Güssregen, Stefan M. Kast
:
The SAMPL6 challenge on predicting octanol-water partition coefficients from EC-RISM theory. 453-461 - Evrim Arslan, Basak Koca Findik
, Viktorya Aviyente
:
A blind SAMPL6 challenge: insight into the octanol-water partition coefficients of drug-like molecules via a DFT approach. 463-470
Volume 34, Number 5, May 2020
- Andreas Krämer
, Phillip S. Hudson, Michael R. Jones, Bernard R. Brooks:
Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge. 471-483 - Michael R. Jones
, Bernard R. Brooks:
Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge. 485-493 - Prajay Patel
, David M. Kuntz, Michael R. Jones, Bernard R. Brooks, Angela K. Wilson
:
SAMPL6 logP challenge: machine learning and quantum mechanical approaches. 495-510 - Davy Guan
, Raymond Lui
, Slade Matthews
:
LogP prediction performance with the SMD solvation model and the M06 density functional family for SAMPL6 blind prediction challenge molecules. 511-522 - Raymond Lui
, Davy Guan
, Slade Matthews
:
A comparison of molecular representations for lipophilicity quantitative structure-property relationships with results from the SAMPL6 logP Prediction Challenge. 523-534 - Samarjeet Prasad
, Bernard R. Brooks:
A deep learning approach for the blind logP prediction in SAMPL6 challenge. 535-542 - Shujie Fan
, Bogdan I. Iorga
, Oliver Beckstein
:
Prediction of octanol-water partition coefficients for the SAMPL6-log P molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields. 543-560 - Marilyn R. Gunner
, Taichi Murakami, Ariën S. Rustenburg, Mehtap Isik
, John D. Chodera:
Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states. 561-573 - Jonathan A. Ouimet, Andrew S. Paluch
:
Predicting octanol/water partition coefficients for the SAMPL6 challenge using the SM12, SM8, and SMD solvation models. 575-588 - Zhaoxi Sun
, Qiao-Le He
, Xiao Li, Zhengdan Zhu
:
SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations. 589-600 - Andrea Rizzi
, Travis Jensen, David R. Slochower
, Matteo Aldeghi
, Vytautas Gapsys
, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen
, Bert L. de Groot
, Zoe Cournia
, Alex Dickson
, Julien Michel
, Michael K. Gilson
, Michael R. Shirts
, David L. Mobley
, John D. Chodera
:
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. 601-633
Volume 34, Number 6, June 2020
- Piero Procacci:
A remark on the efficiency of the double-system/single-box nonequilibrium approach in the SAMPL6 SAMPLing challenge. 635-639 - Vikram Khanna, Jacob I. Monroe
, Michael F. Doherty, Baron Peters
:
Performing solvation free energy calculations in LAMMPS using the decoupling approach. 641-646 - Takeshi Ashida, Takeshi Kikuchi:
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. 647-658 - Edgar López-López
, Obdulia Rabal
, Julen Oyarzabal
, José L. Medina-Franco
:
Towards the understanding of the activity of G9a inhibitors: an activity landscape and molecular modeling approach. 659-669 - Ravi Kumar Rajan
, Muthiah Ramanathan
:
Identification and neuroprotective evaluation of a potential c-Jun N-terminal kinase 3 inhibitor through structure-based virtual screening and in-vitro assay. 671-682 - Petr Kovár, Jakub Skoda, Miroslav Pospísil
, Klára Melánová
, Jan Svoboda
, Ludvík Benes
, Petr Kutálek, Vítezslav Zima
, Filip Bures
:
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. 683-695 - Kamil J. Kuder
, Ilona Michalik
, Katarzyna Kiec-Kononowicz
, Peter Kolb
:
A Taxicab geometry quantification system to evaluate the performance of in silico methods: a case study on adenosine receptors ligands. 697-707
Volume 34, Number 7, July 2020
- Nathan Brown, Peter Ertl
, Richard A. Lewis, Torsten Luksch, Daniel Reker
, Nadine Schneider:
Artificial intelligence in chemistry and drug design. 709-715 - Matthew C. Robinson, Robert C. Glen, Alpha A. Lee
:
Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity prediction. 717-730 - Henry E. Webel
, Talia B. Kimber
, Silke Radetzki
, Martin Neuenschwander
, Marc Nazaré
, Andrea Volkamer
:
Revealing cytotoxic substructures in molecules using deep learning. 731-746 - Darren V. S. Green
, Stephen D. Pickett, Christopher N. Luscombe, Stefan Senger
, David Marcus
, Jamel Meslamani, David Brett, Adam Powell, Jonathan Masson:
BRADSHAW: a system for automated molecular design. 747-765 - Darren V. S. Green
, Stephen D. Pickett, Christopher N. Luscombe, Stefan Senger
, David Marcus
, Jamel Meslamani, David Brett, Adam Powell, Jonathan Masson:
Correction to: BRADSHAW: a system for automated molecular design. 767 - Zhonghua Xia
, Pavel Karpov
, Grzegorz M. Popowicz, Igor V. Tetko
:
Focused Library Generator: case of Mdmx inhibitors. 769-782 - Gian Marco Ghiandoni
, Michael J. Bodkin, Beining Chen, Dimitar Hristozov, James E. A. Wallace, James Webster
, Valerie J. Gillet
:
Enhancing reaction-based de novo design using a multi-label reaction class recommender. 783-803 - Arkadii I. Lin
, Bernd Beck, Dragos Horvath, Gilles Marcou
, Alexandre Varnek
:
Diversifying chemical libraries with generative topographic mapping. 805-815
Volume 34, Number 8, August 2020
- Anjali Soni
, Ruchika Bhat
, Bhyravabhotla Jayaram
:
Improving the binding affinity estimations of protein-ligand complexes using machine-learning facilitated force field method. 817-830 - Anita Rácz, György M. Keserü:
Large-scale evaluation of cytochrome P450 2C9 mediated drug interaction potential with machine learning-based consensus modeling. 831-839 - Muhammad Arif
, Saeed Ahmad
, Farman Ali, Ge Fang, Min Li, Dong-Jun Yu:
TargetCPP: accurate prediction of cell-penetrating peptides from optimized multi-scale features using gradient boost decision tree. 841-856 - Yudibeth Sixto-López
, Martiniano Bello, José Correa-Basurto:
Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach. 857-878 - Huiqun Wang, Bethany A. Reinecke, Yan Zhang
:
Computational insights into the molecular mechanisms of differentiated allosteric modulation at the mu opioid receptor by structurally similar bitopic modulators. 879-895 - Roberto Paciotti
, Mariangela Agamennone
, Cecilia Coletti
, Loriano Storchi
:
Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY approach. 897-914 - Bani Kumar Pathak, Debajyoti Das, Sayan Bhakta, Partha Chakrabarti, Jayati Sengupta:
Resveratrol as a nontoxic excipient stabilizes insulin in a bioactive hexameric form. 915-927
Volume 34, Number 9, September 2020
- Dagmar Stumpfe, Huabin Hu, Jürgen Bajorath
:
Advances in exploring activity cliffs. 929-942 - Huabin Hu, Jürgen Bajorath
:
Simplified activity cliff network representations with high interpretability and immediate access to SAR information. 943-952 - Matthew P. Baumgartner
, David A. Evans
:
Side chain virtual screening of matched molecular pairs: a PDB-wide and ChEMBL-wide analysis. 953-963 - Metin Yazar
, Pemra Ozbek
:
Revisiting allostery in CREB-binding protein (CBP) using residue-based interaction energy. 965-974 - Izudin Redzepovic
, Boris Furtula
:
Predictive potential of eigenvalue-based topological molecular descriptors. 975-982 - Manish Kumar Tripathi
, Piyoosh Sharma
, Avanish Tripathi
, Prabhash Nath Tripathi
, Pavan Srivastava, Ankit Seth
, Sushant Kumar Shrivastava
:
Computational exploration and experimental validation to identify a dual inhibitor of cholinesterase and amyloid-beta for the treatment of Alzheimer's disease. 983-1002 - Shalini Thiruchittampalam
, Samantha Weerasinghe
:
Plausible compounds drawn from plants as curative agents for neurodegeneration: An in-silico approach. 1003-1011
Volume 34, Number 10, October 2020
- Raquel Rodríguez-Pérez
, Jürgen Bajorath
:
Interpretation of machine learning models using shapley values: application to compound potency and multi-target activity predictions. 1013-1026 - Gregory L. Szwabowski
, Paige N. Castleman, Chandler K. Sears, Lee H. Wink, Judith A. Cole, Daniel L. Baker
, Abby L. Parrill
:
Benchmarking GPCR homology model template selection in combination with de novo loop generation. 1027-1044 - Almudena Perona
, M. Piedad Ros, Alberto Mills
, Antonio Morreale
, Federico Gago
:
Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor H1. 1045-1062 - Isaias Lans, Karen Palacio-Rodríguez
, Claudio N. Cavasotto
, Pilar Cossio
:
Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles. 1063-1077 - José L. Borioni
, Valeria Cavallaro
, Adriana B. Pierini, Ana Paula Murray
, Alicia B. Peñéñory, Marcelo Puiatti
, Manuela E. García:
An activity prediction model for steroidal and triterpenoidal inhibitors of Acetylcholinesterase enzyme. 1079-1090 - Natalie M. Colodette, Lucas S. Franco, Rodolfo C. Maia, Harold H. Fokoue, Carlos Mauricio R. Sant'Anna
, Eliezer J. Barreiro
:
Novel phosphatidylinositol 4-kinases III beta (PI4KIIIβ) inhibitors discovered by virtual screening using free energy models. 1091-1103 - Phasit Charoenkwan, Chanin Nantasenamat
, Md. Mehedi Hasan
, Watshara Shoombuatong
:
Meta-iPVP: a sequence-based meta-predictor for improving the prediction of phage virion proteins using effective feature representation. 1105-1116
Volume 34, Number 11, November 2020
- Robert D. Clark
, Denise N. Morris, Gary Chinigo, Michael S. Lawless, Jacques Prudhomme, Karine G. Le Roch
, Maria José Lafuente, Santiago Ferrer
, Francisco Javier Gamo, Robert Gadwood, Walter S. Woltosz:
Design and tests of prospective property predictions for novel antimalarial 2-aminopropylaminoquinolones. 1117-1132 - Mei Qian Yau
, Abigail L. Emtage
, Jason S. E. Loo
:
Benchmarking the performance of MM/PBSA in virtual screening enrichment using the GPCR-Bench dataset. 1133-1145 - Ammar Abdo
, Eissa Ghaleb, Naser K. A. Alajmi, Maude Pupin
:
Monomer structure fingerprints: an extension of the monomer composition version for peptide databases. 1147-1156 - Denis B. Tikhonov
, Lianyun Lin, Daniel S. C. Yang, Zhiguang Yuchi, Boris S. Zhorov:
Phenylalkylamines in calcium channels: computational analysis of experimental structures. 1157-1169 - Marianna Bufano
, Marion Laudette
, Jean-Paul Blondeau
, Frank Lezoualc'h
, Marianna Nalli
, Romano Silvestri
, Andrea Brancale
, Antonio Coluccia
:
Modeling Epac1 interactions with the allosteric inhibitor AM-001 by co-solvent molecular dynamics. 1171-1179 - Silvia Atanasio, Giuseppe Deganutti
, Christopher A. Reynolds
:
Addressing free fatty acid receptor 1 (FFAR1) activation using supervised molecular dynamics. 1181-1193 - Kai Liu
, Hironori Kokubo
:
Prediction of ligand binding mode among multiple cross-docking poses by molecular dynamics simulations. 1195-1205
Volume 34, Number 12, December 2020
- Dimitar G. Yonchev
, Jürgen Bajorath
:
DeepCOMO: from structure-activity relationship diagnostics to generative molecular design using the compound optimization monitor methodology. 1207-1218 - Brian Olson
, Anthony Cruz-Balberdy
, Lieyang Chen, Mossa Ghattas
, Yeonji Ji, Kunhui Huang, Steven Ayoub, Tyler Luchko
, Daniel J. McKay, Tom Kurtzman
:
An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets. 1219-1228 - Mst. Shamima Khatun, Md. Mehedi Hasan
, Watshara Shoombuatong, Hiroyuki Kurata
:
ProIn-Fuse: improved and robust prediction of proinflammatory peptides by fusing of multiple feature representations. 1229-1236 - Sara Sarfaraz
, Iqra Muneer, Haiyan Liu
:
Combining fragment docking with graph theory to improve ligand docking for homology model structures. 1237-1259 - Hossein Aghazadeh
, Mokhtar Ganjali Koli
, Reza Ranjbar, Kamran Pooshang Bagheri
:
Interactions of GF-17 derived from LL-37 antimicrobial peptide with bacterial membranes: a molecular dynamics simulation study. 1261-1273 - Julián A. Bélgamo, Lucas N. Alberca, Jorge L. Pórfido
, Franco N. Caram Romero, Santiago Rodriguez
, Alan Talevi, Betina Córsico, Gisela R. Franchini
:
Application of target repositioning and in silico screening to exploit fatty acid binding proteins (FABPs) from Echinococcus multilocularis as possible drug targets. 1275-1288 - Jianzhong Chen
, Wei Wang, Haibo Sun, Laixue Pang, Baohua Yin:
Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics. 1289-1305

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