Comparative evaluation of eight docking tools for docking and virtual screening accuracy

TLDR

The study compared eight docking programs (DOCK, FLEXX, FRED, GLIDE, GOLD, SLIDE, SURFLEX, and QXP) on their ability to recover X‑ray poses of 100 small‑molecule ligands and to discriminate thymidine kinase inhibitors from random drug‑like molecules. The best docking accuracy tools (GLIDE, GOLD, SURFLEX) also ranked known inhibitors most successfully, and the study identified ligand and binding‑site physicochemical descriptors that generally cause docking/scoring errors. © 2004 Wiley‑Liss, Inc., Proteins 2004.

Abstract

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.