title: Comparative evaluation of eight docking tools for docking and virtual screening accuracy.
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.
authors.affiliation: Bioinformatics Group, Laboratoire de Pharmacochimie de la Communication Cellulaire, CNRS UMR7081 Illkirch, France.
authors.forename: Esther
authors.initials: E
authors.lastname: Kellenberger
authors.forename: Jordi
authors.initials: J
authors.lastname: Rodrigo
authors.forename: Pascal
authors.initials: P
authors.lastname: Muller
authors.forename: Didier
authors.initials: D
authors.lastname: Rognan
mesh_terms: 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
chemical_list: D008024:Ligands; D014764:Viral Proteins; D013937:Thymidine Kinase