Volume 32, Issue 1 | Journal of Computer-Aided Molecular Design

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Volume 32, Issue 1

January 2018

Special Issue: Drug Discovery Data Resource Grand Challenge 2 (D3RGC2)

Issue Editors:

Rommie E Amaro,
Michael K. Gilson

24 articles in this issue

D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
Zied Gaieb
Shuai Liu
Rommie E. Amaro
OriginalPaper 04 December 2017 Pages: 1 - 20
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
Christina Athanasiou
Sofia Vasilakaki
Zoe Cournia
OriginalPaper 08 November 2017 Pages: 21 - 44
Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2
Matthew P. Baumgartner
David A. Evans
OriginalPaper 10 November 2017 Pages: 45 - 58
Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling
Soumendranath Bhakat
Emil Åberg
Pär Söderhjelm
OriginalPaper Open access 20 October 2017 Pages: 59 - 73
Ranking docking poses by graph matching of protein–ligand interactions: lessons learned from the D3R Grand Challenge 2
Priscila da Silva Figueiredo Celestino Gomes
Franck Da Silva
Didier Rognan
OriginalPaper 01 August 2017 Pages: 75 - 87
CDOCKER and \(\lambda\)-dynamics for prospective prediction in D3R Grand Challenge 2
Xinqiang Ding
Ryan L. Hayes
Charles L. Brooks III
OriginalPaper 07 September 2017 Pages: 89 - 102
Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor
Rui Duan
Xianjin Xu
Xiaoqin Zou
OriginalPaper 10 November 2017 Pages: 103 - 111
Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016
Xavier Fradera
Andreas Verras
Ying-Duo Gao
OriginalPaper 14 September 2017 Pages: 113 - 127
Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort
Ying-Duo Gao
Yuan Hu
Zhengwei Peng
OriginalPaper 06 October 2017 Pages: 129 - 142
Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method
Hervé Hogues
Traian Sulea
Enrico O. Purisima
OriginalPaper 05 October 2017 Pages: 143 - 150
Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2
Maria Kadukova
Sergei Grudinin
OriginalPaper 14 September 2017 Pages: 151 - 162
A cross docking pipeline for improving pose prediction and virtual screening performance
Ashutosh Kumar
Kam Y. J. Zhang
OriginalPaper 23 August 2017 Pages: 163 - 173
Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2
Zeynep Kurkcuoglu
Panagiotis I. Koukos
A. M. J. J. Bonvin
OriginalPaper Open access 22 August 2017 Pages: 175 - 185
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach
Polo C.-H. Lam
Ruben Abagyan
Maxim Totrov
OriginalPaper Open access 08 September 2017 Pages: 187 - 198
Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations
Antonia S. J. S. Mey
Jordi Juárez Jiménez
Julien Michel
OriginalPaper Open access 13 November 2017 Pages: 199 - 210
Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking
Martin A. Olsson
Alfonso T. García-Sosa
Ulf Ryde
OriginalPaper Open access 06 September 2017 Pages: 211 - 224
Protein–ligand docking using FFT based sampling: D3R case study
Dzmitry Padhorny
David R. Hall
Dima Kozakov
OriginalPaper 03 November 2017 Pages: 225 - 230
Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study
Manon Réau
Florent Langenfeld
Matthieu Montes
OriginalPaper 14 September 2017 Pages: 231 - 238
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
Eko Aditya Rifai
Marc van Dijk
Daan P. Geerke
OriginalPaper Open access 09 September 2017 Pages: 239 - 249
Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2
Veronica Salmaso
Mattia Sturlese
Stefano Moro
OriginalPaper 24 August 2017 Pages: 251 - 264
Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP+
Christina Schindler
Friedrich Rippmann
Daniel Kuhn
OriginalPaper 12 September 2017 Pages: 265 - 272
Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations
Edithe Selwa
Eddy Elisée
Bogdan I. Iorga
OriginalPaper 02 September 2017 Pages: 273 - 286
Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges
Bentley M. Wingert
Rick Oerlemans
Carlos J. Camacho
OriginalPaper 16 September 2017 Pages: 287 - 297
Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations
Oleksandr Yakovenko
Steven J. M. Jones
OriginalPaper Open access 13 November 2017 Pages: 299 - 311