Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance

vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available

(2016) Ludovic Chaput et al.   Journal of Cheminformatics

Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives

(2015) Nathalie Lagarde et al.   Journal of Chemical Information and Modeling

Beware of docking!

(2015) Yu-Chian Chen   TRENDS IN PHARMACOLOGICAL SCIENCES

Surflex-Dock: Docking benchmarks and real-world application

(2012) Russell Spitzer et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A consistent description of HYdrogen bond and DEhydration energies in protein–ligand complexes: methods behind the HYDE scoring function

(2012) Nadine Schneider et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test

(2012) John W. Liebeschuetz et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Docking and scoring with ICM: the benchmarking results and strategies for improvement

(2012) Marco A. C. Neves et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Analysis of multiple compound-protein interactions reveals novel bioactive molecules

(2011) H. Yabuuchi et al.   Molecular Systems Biology

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods

(2010) Jianxin Duan et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Molecular Docking Screens Using Comparative Models of Proteins

(2009) Hao Fan et al.   Journal of Chemical Information and Modeling

Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy

(2009) Jason B. Cross et al.   Journal of Chemical Information and Modeling

How to do an evaluation: pitfalls and traps

(2008) Paul C. D. Hawkins et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?

(2008) Andrew C. Good et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Community benchmarks for virtual screening

(2008) John J. Irwin   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN