Volume 30, Issue 9 | Journal of Computer-Aided Molecular Design

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Volume 30, Issue 9

September 2016

Special Issue: Drug Design Data Resource Grand Challenge 2015

Issue Editor:

W. Patrick Walters

14 articles in this issue

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions
Symon Gathiaka
Shuai Liu
Michael K. Gilson
OriginalPaper 30 September 2016 Pages: 651 - 668
Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015
Inna Slynko
Franck Da Silva
Didier Rognan
OriginalPaper 01 August 2016 Pages: 669 - 683
Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015
Ashutosh Kumar
Kam Y. J. Zhang
OriginalPaper 02 August 2016 Pages: 685 - 693
Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge
Zhaofeng Ye
Matthew P. Baumgartner
Carlos J. Camacho
OriginalPaper 29 August 2016 Pages: 695 - 706
Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations
Majda Misini Ignjatović
Octav Caldararu
Ulf Ryde
OriginalPaper Open access 26 August 2016 Pages: 707 - 730
Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015
Diogo Santos-Martins
OriginalPaper 22 August 2016 Pages: 731 - 742
Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015
Nanjie Deng
William F. Flynn
Ronald M. Levy
OriginalPaper 25 August 2016 Pages: 743 - 751
Yada: a novel tool for molecular docking calculations
S. Piotto
L. Di Biasi
S. Concilio
OriginalPaper 26 August 2016 Pages: 753 - 759
A D3R prospective evaluation of machine learning for protein-ligand scoring
Jocelyn Sunseri
Matthew Ragoza
David Ryan Koes
OriginalPaper 03 September 2016 Pages: 761 - 771
DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015
Veronica Salmaso
Mattia Sturlese
Stefano Moro
OriginalPaper 16 September 2016 Pages: 773 - 789
Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation
Sergei Grudinin
Maria Kadukova
Frédéric Cazals
OriginalPaper 07 October 2016 Pages: 791 - 804
Docking-undocking combination applied to the D3R Grand Challenge 2015
Sergio Ruiz-Carmona
Xavier Barril
OriginalPaper 05 October 2016 Pages: 805 - 815
Improved pose and affinity predictions using different protocols tailored on the basis of data availability
Philip Prathipati
Chioko Nagao
Kenji Mizuguchi
OriginalPaper 06 October 2016 Pages: 817 - 828
Molecular docking performance evaluated on the D3R Grand Challenge 2015 drug-like ligand datasets
Edithe Selwa
Virginie Y. Martiny
Bogdan I. Iorga
OriginalPaper 03 October 2016 Pages: 829 - 839