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Journal of Computer-Aided Molecular Design, Volume 32
Volume 32, Number 1, January 2018
- Zied Gaieb, Shuai Liu, Symon Gathiaka, Michael Chiu
, Huanwang Yang, Chenghua Shao
, Victoria A. Feher, W. Patrick Walters, Bernd Kuhn, Markus G. Rudolph, Stephen K. Burley, Michael K. Gilson, Rommie E. Amaro
:
D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. 1-20 - Christina Athanasiou
, Sofia Vasilakaki
, Dimitris Dellis, Zoe Cournia
:
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. 21-44 - Matthew P. Baumgartner
, David A. Evans:
Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2. 45-58 - Soumendranath Bhakat
, Emil Åberg, Pär Söderhjelm
:
Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling. 59-73 - Priscila da Silva Figueiredo Celestino Gomes
, Franck Da Silva, Guillaume Bret, Didier Rognan
:
Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2. 75-87 - Xinqiang Ding, Ryan L. Hayes, Jonah Z. Vilseck, Murchtricia K. Charles, Charles L. Brooks III
:
CDOCKER and λ-dynamics for prospective prediction in D3R Grand Challenge 2. 89-102 - Rui Duan
, Xianjin Xu
, Xiaoqin Zou
:
Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor. 103-111 - Xavier Fradera
, Andreas Verras
, Yuan Hu
, Deping Wang, Hongwu Wang, James I. Fells, Kira A. Armacost, Alejandro Crespo, Brad Sherborne, Huijun Wang, Zhengwei Peng, Ying-Duo Gao:
Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016. 113-127 - Ying-Duo Gao, Yuan Hu
, Alejandro Crespo, Deping Wang, Kira A. Armacost, James I. Fells, Xavier Fradera, Hongwu Wang, Huijun Wang, Brad Sherborne, Andreas Verras, Zhengwei Peng:
Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort. 129-142 - Hervé Hogues, Traian Sulea, Francis Gaudreault, Christopher R. Corbeil
, Enrico O. Purisima:
Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method. 143-150 - Maria Kadukova
, Sergei Grudinin
:
Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2. 151-162 - Ashutosh Kumar, Kam Y. J. Zhang
:
A cross docking pipeline for improving pose prediction and virtual screening performance. 163-173 - Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikael E. Trellet, João P. G. L. M. Rodrigues, Irina S. Moreira
, Jorge Roel-Touris, Adrien S. J. Melquiond
, Cunliang Geng
, Jörg Schaarschmidt
, Li C. Xue, Anna Vangone
, Alexandre M. J. J. Bonvin
:
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. 175-185 - Polo Chun-Hung Lam, Ruben Abagyan, Maxim Totrov
:
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach. 187-198 - Antonia S. J. S. Mey, Jordi Juárez Jiménez, Julien Michel:
Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations. 199-210 - Martin A. Olsson, Alfonso T. García-Sosa
, Ulf Ryde
:
Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking. 211-224 - Dzmitry Padhorny, David R. Hall, Hanieh Mirzaei, Artem B. Mamonov, Mohammad Moghadasi, Andrey Alekseenko
, Dmitri Beglov, Dima Kozakov
:
Protein-ligand docking using FFT based sampling: D3R case study. 225-230 - Manon Réau
, Florent Langenfeld
, Jean-François Zagury, Matthieu Montès
:
Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study. 231-238 - Eko Aditya Rifai
, Marc van Dijk
, Nico P. E. Vermeulen
, Daan P. Geerke
:
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. 239-249 - Veronica Salmaso
, Mattia Sturlese
, Alberto Cuzzolin, Stefano Moro
:
Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2. 251-264 - Christina E. M. Schindler, Friedrich Rippmann, Daniel Kuhn:
Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP+. 265-272 - Edithe Selwa, Eddy Elisée
, Agustin Zavala
, Bogdan I. Iorga
:
Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations. 273-286 - Bentley M. Wingert
, Rick Oerlemans
, Carlos J. Camacho:
Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges. 287-297 - Oleksandr Yakovenko, Steven J. M. Jones
:
Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations. 299-311
Volume 32, Number 2, February 2018
- Johann Gasteiger, Yvonne C. Martin, Anthony Nicholls, Tudor I. Oprea
, Terry R. Stouch:
Leaving us with fond memories, smiles, SMILES and, alas, tears: a tribute to David Weininger, 1952-2016. 313-319 - Ryo Kunimoto
, Jürgen Bajorath
:
Design of a tripartite network for the prediction of drug targets. 321-330 - Zoltán Orgován, György G. Ferenczy
, Thomas Steinbrecher, Bence Szilágyi
, Dávid Bajusz
, György M. Keserü
:
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. 331-345 - Miao Yu, Qiong Gu
, Jun Xu
:
Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening. 347-361 - Natalia Nikitina
, Evgeny Ivashko
, Andrei Tchernykh
:
Congestion game scheduling for virtual drug screening optimization. 363-374 - Mohammad Amin Valizade Hasanloei
, Razieh Sheikhpour
, Mehdi Agha Sarram, Elnaz Sheikhpour, Hamdollah Sharifi:
A combined Fisher and Laplacian score for feature selection in QSAR based drug design using compounds with known and unknown activities. 375-384 - Stefano Della-Longa
, Alessandro Arcovito
:
"In silico" study of the binding of two novel antagonists to the nociceptin receptor. 385-400
Volume 32, Number 3, March 2018
- Timur Gimadiev, Timur I. Madzhidov
, Ramil I. Nugmanov
, Igor I. Baskin
, Igor S. Antipin
, Alexandre Varnek
:
Assessment of tautomer distribution using the condensed reaction graph approach. 401-414 - Sebastian Raschka, Anne M. Scott, Nan Liu, Santosh Gunturu, Mar Huertas, Weiming Li, Leslie A. Kuhn
:
Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control. 415-433 - Manuela Sabatino, Dante Rotili, Alexandros Patsilinakos
, Mariantonietta Forgione, Daniela Tomaselli, Fréderic Alby, Paola B. Arimondo, Antonello Mai, Rino Ragno
:
Disruptor of telomeric silencing 1-like (DOT1L): disclosing a new class of non-nucleoside inhibitors by means of ligand-based and structure-based approaches. 435-458 - Zainab K. Sanusi, Thavendran Govender
, Glenn E. M. Maguire, Sibusiso B. Maseko, Johnson Lin
, Hendrik G. Kruger
, Bahareh Honarparvar
:
An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant. 459-471 - Stefania Villa
, Laura Legnani
, Diego Colombo
, Arianna Gelain
, Carmen Lammi
, Daniele Bongiorno
, Denise P. Ilboudo
, Kellen E. McGee
, Jürgen Bosch
, Giovanni Grazioso
:
Structure-based drug design, synthesis and biological assays of P. falciparum Atg3-Atg8 protein-protein interaction inhibitors. 473-486 - Krishna P. Singh
, Lokesh Baweja, Olaf Wolkenhauer, Qamar Rahman, Shailendra K. Gupta
:
Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide. 487-496
Volume 32, Number 4, April 2018
- David A. Winkler:
Sparse QSAR modelling methods for therapeutic and regenerative medicine. 497-509 - Sebastian Raschka, Alex J. Wolf, Joseph Bemister-Buffington, Leslie A. Kuhn
:
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. 511-528 - Francesco Manzoni, Ulf Ryde
:
Assessing the stability of free-energy perturbation calculations by performing variations in the method. 529-536 - Peter A. Hunt
, Matthew D. Segall, Jonathan D. Tyzack
:
WhichP450: a multi-class categorical model to predict the major metabolising CYP450 isoform for a compound. 537-546 - Jian Gao
, Li Liang, Qingqing Chen, Ling Zhang, Tonghui Huang:
Insight into the molecular mechanism of yeast acetyl-coenzyme A carboxylase mutants F510I, N485G, I69E, E477R, and K73R resistant to soraphen A. 547-557 - Shubhandra Tripathi
, Gaurava Srivastava
, Aastha Singh, A. P. Prakasham
, Arvind S. Negi, Ashok Sharma:
Insight into microtubule destabilization mechanism of 3, 4, 5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis. 559-572 - Xin Zhang
, Jason B. Cross, Jan Romero, Alexander Heifetz, Eric Humphries, Katie Hall, Yuchuan Wu, Sabrina Stucka, Jing Zhang, Haoqun Chandonnet, Blaise Lippa, M. Dominic Ryan, J. Christian Baber:
In-silico guided discovery of novel CCR9 antagonists. 573-582
Volume 32, Number 5, May 2018
- Sankalp Jain
, Eleni Kotsampasakou, Gerhard F. Ecker:
Comparing the performance of meta-classifiers - a case study on selected imbalanced data sets relevant for prediction of liver toxicity. 583-590 - Luan Carvalho Martins
, Pedro Henrique Monteiro Torres
, Renata Barbosa de Oliveira
, Pedro Geraldo Pascutti
, Elio A. Cino
, Rafaela Salgado Ferreira
:
Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations. 591-605 - Érica C. M. Nascimento
, Mónica Oliva
, Juan Andrés
:
Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase. 607-622 - Francesca Cardamone, Mattia Falconi
, Alessandro Desideri
:
Molecular dynamics characterization of the SAMHD1 Aicardi-Goutières Arg145Gln mutant: structural determinants for the impaired tetramerization. 623-632 - Lu Lu, Hua Yu
:
DR2DI: a powerful computational tool for predicting novel drug-disease associations. 633-642 - Songling Ma, Jiwon Choi, Xuemei Jin, Hyun-Yi Kim, Jihye Yun, Weontae Lee
, Kang-Yell Choi, Kyoung Tai No
:
Discovery of a small-molecule inhibitor of Dvl-CXXC5 interaction by computational approaches. 643-655
Volume 32, Number 6, June 2018
- Mazen Y. Hamed:
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. 657-669 - Timothy Cholko
, Wei Chen, Zhiye Tang
, Chia-en A. Chang:
A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery. 671-685 - Thandokuhle Ntombela, Zeynab Fakhar
, Collins U. Ibeji, Thavendran Govender
, Glenn E. M. Maguire, Gyanu Lamichhane, Hendrik G. Kruger
, Bahareh Honarparvar
:
Molecular insight on the non-covalent interactions between carbapenems and l, d-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study. 687-701 - Erick Martins Ratamero, Dom Bellini, Christopher G. Dowson
, Rudolf A. Römer
:
Touching proteins with virtual bare hands - Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware. 703-709 - Sofja Tshepelevitsh
, Kertu Hernits, Ivo Leito
:
Prediction of partition and distribution coefficients in various solvent pairs with COSMO-RS. 711-722
Volume 32, Number 7, July 2018
- Dimitris K. Agrafiotis, M. Katharine Holloway, Scott A. Johnson
, Charles H. Reynolds, Terry R. Stouch, Alexander Tropsha, Chris L. Waller:
Chemistry, information and Frank: a tribute to Frank Brown. 723-729 - Ann E. Cleves
, Ajay N. Jain
:
Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose. 731-757 - Tomoyuki Miyao, Jürgen Bajorath
:
Exploring ensembles of bioactive or virtual analogs of X-ray ligands for shape similarity searching. 759-767 - Saveliy Belkin
, Petras J. Kundrotas, Ilya A. Vakser:
Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking. 769-779 - Marcela Vettorazzi, Cintia Menéndez, Lucas Gutierrez, Sebastian A. Andujar, Gustavo Appignanesi, Ricardo D. Enriz
:
Theoretical models to predict the inhibitory effect of ligands of sphingosine kinase 1 using QTAIM calculations and hydrogen bond dynamic propensity analysis. 781-791 - Shibaji Ghosh, Kalyanashis Jana
, Bishwajit Ganguly
:
Influence of gauche effect on uncharged oxime reactivators for the reactivation of tabun-inhibited AChE: quantum chemical and steered molecular dynamics studies. 793-807
Volume 32, Number 8, August 2018
- Yvonne C. Martin:
How medicinal chemists learned about log P. 809-819 - Hemavathy Nagarajan, Umashankar Vetrivel:
Demystifying the pH dependent conformational changes of human heparanase pertaining to structure-function relationships: an in silico approach. 821-840 - Matthew Habgood:
Conformational ensemble comparison for small molecules in drug discovery. 841-852 - Minh Khoa Nguyen, Léonard Jaillet, Stéphane Redon
:
Generating conformational transition paths with low potential-energy barriers for proteins. 853-867 - Mauricio Carrillo-Tripp
, Leonardo Alvarez-Rivera, Omar Israel Lara-Ramírez, Francisco Javier Becerra-Toledo, Adan Vega-Ramírez, Emmanuel Quijas-Valades, Eduardo González-Zavala, Julio Cesar González-Vázquez, Javier García-Vieyra, Nelly Beatriz Santoyo-Rivera, Sergio Víctor Chapa Vergara, Amilcar Meneses Viveros
:
HTMoL: full-stack solution for remote access, visualization, and analysis of molecular dynamics trajectory data. 869-876
Volume 32, Number 9, September 2018
- Michael Zhenin, Malkeet Singh Bahia, Gilles Marcou
, Alexandre Varnek, Hanoch Senderowitz, Dragos Horvath
:
Rescoring of docking poses under Occam's Razor: are there simpler solutions? 877-888 - D. Sam Paul
, N. Gautham:
Protein-small molecule docking with receptor flexibility in iMOLSDOCK. 889-900 - Yaping Li, Yinglan Pu, Hui Liu, Li Zhang, Xingyong Liu, Yan Li, Zhili Zuo
:
Discovery of novel wee1 inhibitors via structure-based virtual screening and biological evaluation. 901-915 - Jie Chen, Xiao Lin, Kyoung Jin Park, Kang Ro Lee, Hyun-Ju Park
:
Identification of protoberberine alkaloids as novel histone methyltransferase G9a inhibitors by structure-based virtual screening. 917-928 - Piya Patra, Mahua Ghosh, Raja Banerjee, Jaydeb Chakrabarti
:
Quantum chemical studies on anion specificity of CαNN motif in functional proteins. 929-936
Volume 32, Number 10, October 2018
- Andrea Rizzi
, Steven Murkli
, John N. McNeill
, Wei Yao
, Matthew R. Sullivan
, Michael K. Gilson
, Michael Chiu, Lyle Isaacs
, Bruce C. Gibb
, David L. Mobley
, John D. Chodera
:
Overview of the SAMPL6 host-guest binding affinity prediction challenge. 937-963 - Piero Procacci
, Massimiliano Guarrasi, Guido Guarnieri
:
SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach. 965-982 - Phillip S. Hudson
, Kyungreem Han
, H. Lee Woodcock III
, Bernard R. Brooks
:
Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. 983-999 - Tom Dixon, Samuel D. Lotz, Alex Dickson
:
Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge. 1001-1012 - Lin Frank Song, Nupur Bansal
, Zheng Zheng, Kenneth M. Merz Jr.
:
Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge. 1013-1026 - Octav Caldararu, Martin A. Olsson, Majda Misini Ignjatovic, Meiting Wang, Ulf Ryde
:
Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods. 1027-1046 - Michail Papadourakis, Stefano Bosisio, Julien Michel
:
Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge. 1047-1058 - Kyungreem Han
, Phillip S. Hudson
, Michael R. Jones
, Naohiro Nishikawa
, Florentina Tofoleanu
, Bernard R. Brooks
:
Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method. 1059-1073 - Naohiro Nishikawa
, Kyungreem Han
, Xiongwu Wu
, Florentina Tofoleanu
, Bernard R. Brooks
:
Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges. 1075-1086 - Marie L. Laury
, Zhi Wang
, Aaron S. Gordon, Jay W. Ponder
:
Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field. 1087-1095 - Yigitcan Eken
, Prajay Patel
, Thomas Díaz, Michael R. Jones, Angela K. Wilson
:
SAMPL6 host-guest challenge: binding free energies via a multistep approach. 1097-1115 - Mehtap Isik, Dorothy Levorse, Ariën S. Rustenburg, Ikenna E. Ndukwe, Heather Wang, Xiao Wang, Mikhail Y. Reibarkh
, Gary E. Martin, Alexey A. Makarov
, David L. Mobley
, Timothy Rhodes, John D. Chodera
:
pK a measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. 1117-1138 - Philipp Pracht
, Rainer Wilcken, Anikó Udvarhelyi
, Stephane Rodde, Stefan Grimme:
High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge. 1139-1149 - Nicolas Tielker, Lukas Eberlein, Stefan Güssregen, Stefan M. Kast
:
The SAMPL6 challenge on predicting aqueous pK a values from EC-RISM theory. 1151-1163 - Caitlin C. Bannan
, David L. Mobley
, A. Geoffrey Skillman:
SAMPL6 challenge results from a predictions based on a general Gaussian process model. 1165-117 - Qiao Zeng
, Michael R. Jones, Bernard R. Brooks:
Absolute and relative pK a predictions via a DFT approach applied to the SAMPL6 blind challenge. 1179-1189 - Samarjeet Prasad
, Jing Huang
, Qiao Zeng, Bernard R. Brooks:
An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge. 1191-1201 - Edithe Selwa, Ian M. Kenney, Oliver Beckstein
, Bogdan I. Iorga
:
SAMPL6: calculation of macroscopic pK a values from ab initio quantum mechanical free energies. 1203-1216
Volume 32, Number 11, November 2018
- Youlin Xue
, Qiaoshi Zhang, Yuna Sun, Xiaohong Zhou, Ian P. Hurley, Gary W. Jones
, Youtao Song:
Using steered molecular dynamics to study the interaction between ADP and the nucleotide-binding domain of yeast Hsp70 protein Ssa1. 1217-1227 - Noriyuki Yamaotsu
, Shuichi Hirono:
In silico fragment-mapping method: a new tool for fragment-based/structure-based drug discovery. 1229-1245 - Irena Majerz
:
Weak interactions in furan dimers. 1247-1258 - Paulo Siani
, Himanshu Khandelia
, M. Orsi, Luis Gustavo Dias
:
Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics. 1259-1271 - Gonzalo Cerruela García
, Nicolás García-Pedrajas:
Boosted feature selectors: a case study on prediction P-gp inhibitors and substrates. 1273-1294 - Laurence Leherte
, Axel Petit, Denis Jacquemin
, Daniel P. Vercauteren
, Adèle D. Laurent
:
Investigating cyclic peptides inhibiting CD2-CD58 interactions through molecular dynamics and molecular docking methods. 1295-1313
Volume 32, Number 12, December 2018
- Julio Caballero
, Alejandro Morales-Bayuelo, Carlos Navarro-Retamal:
Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors. 1315-1336 - Enrico Margiotta
, Giuseppe Deganutti
, Stefano Moro
:
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. 1337-1346 - E. Srinivasan
, R. Rajasekaran
:
Quantum chemical and molecular mechanics studies on the assessment of interactions between resveratrol and mutant SOD1 (G93A) protein. 1347-1361 - Wen Hu, Liu Qin, Menglong Li, Xuemei Pu, Yanzhi Guo:
Individually double minimum-distance definition of protein-RNA binding residues and application to structure-based prediction. 1363-1373 - Stefan A. P. Lenz, Stacey D. Wetmore
:
Structural explanation for the tunable substrate specificity of an E. coli nucleoside hydrolase: insights from molecular dynamics simulations. 1375-1388
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