Premium
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
Author(s) -
Kellenberger Esther,
Rodrigo Jordi,
Muller Pascal,
Rognan Didier
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20149
Subject(s) - docking (animal) , virtual screening , computer science , protein–ligand docking , medicine , bioinformatics , biology , drug discovery , nursing
Abstract Eight docking programs (DOCK, FLEXX, FRED, GLIDE, GOLD, SLIDE, SURFLEX, and QXP) that can be used for either single‐ligand docking or database screening have been compared for their propensity to recover the X‐ray pose of 100 small‐molecular‐weight ligands, and for their capacity to discriminate known inhibitors of an enzyme (thymidine kinase) from randomly chosen “drug‐like” molecules. Interestingly, both properties are found to be correlated, since the tools showing the best docking accuracy (GLIDE, GOLD, and SURFLEX) are also the most successful in ranking known inhibitors in a virtual screening experiment. Moreover, the current study pinpoints some physicochemical descriptors of either the ligand or its cognate protein‐binding site that generally lead to docking/scoring inaccuracies. Proteins 2004. © 2004 Wiley‐Liss, Inc.