Comparative evaluation of eight docking tools for docking and virtual screening accuracy.
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.
Kellenberger
Esther
E
Bioinformatics Group, Laboratoire de Pharmacochimie de la Communication Cellulaire, CNRS UMR7081 Illkirch, France.
Rodrigo
Jordi
J
Muller
Pascal
P
Rognan
Didier
D
D003196:Computer Graphics / Q000592:standards*; D018360:Crystallography, X-Ray; D030562:Databases, Protein / Q000592:standards; D015195:Drug Design; D018259:Herpesvirus 1, Human / Q000737:chemistry / Q000201:enzymology; D046609:Libraries, Digital / Q000592:standards; D008024:Ligands; D020836:Protein Structure, Quaternary; D012984:Software / Q000592:standards*; D013937:Thymidine Kinase / Q000737:chemistry; D014584:User-Computer Interface; D014764:Viral Proteins / Q000737:chemistry
D008024:Ligands; D014764:Viral Proteins; D013937:Thymidine Kinase