D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings

Ensemble Docking in Drug Discovery

(2018) Rommie E. Amaro et al.   BIOPHYSICAL JOURNAL

Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes

(2018) Shahrooz Zarbafian et al.   Scientific Reports

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

(2018) Zixuan Cang et al.   PLoS Computational Biology

Multiscale methods in drug design bridge chemical and biological complexity in the search for cures

(2018) Rommie E. Amaro et al.   Nature Reviews Chemistry

D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2017) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Progress towards a public chemogenomic set for protein kinases and a call for contributions

(2017) David H. Drewry et al.   PLoS One

Lessons Learned over Four Benchmark Exercises from the Community Structure–Activity Resource

(2016) Heather A. Carlson   Journal of Chemical Information and Modeling

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

(2016) Heather A. Carlson et al.   Journal of Chemical Information and Modeling

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

(2016) Symon Gathiaka et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A pose prediction approach based on ligand 3D shape similarity

(2016) Ashutosh Kumar et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Docking Screens for Novel Ligands Conferring New Biology

(2016) John J. Irwin et al.   JOURNAL OF MEDICINAL CHEMISTRY

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Advances in Activity Cliff Research

(2016) Dilyana Dimova et al.   Molecular Informatics

Role of computer-aided drug design in modern drug discovery

(2015) Stephani Joy Y. Macalino et al.   ARCHIVES OF PHARMACAL RESEARCH

POSIT: Flexible Shape-Guided Docking For Pose Prediction

(2015) Brian P. Kelley et al.   Journal of Chemical Information and Modeling

CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series

(2013) Kelly L. Damm-Ganamet et al.   Journal of Chemical Information and Modeling

Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise

(2013) David Ryan Koes et al.   Journal of Chemical Information and Modeling

Potential and Limitations of Ensemble Docking

(2012) Oliver Korb et al.   Journal of Chemical Information and Modeling

CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions

(2011) Richard D. Smith et al.   Journal of Chemical Information and Modeling

Protein Kinases: Docking and Homology Modeling Reliability

(2010) Tiziano Tuccinardi et al.   Journal of Chemical Information and Modeling

Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions

(2010) Sheng-You Huang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Lead Finder: An Approach To Improve Accuracy of Protein−Ligand Docking, Binding Energy Estimation, and Virtual Screening

(2008) Oleg V. Stroganov et al.   Journal of Chemical Information and Modeling

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

(2008) Rommie E. Amaro et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN