Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites.

ABSTRACT: The use of predicted binding sites (binding sites calculated from the protein structure alone) is evaluated here as a tool to focus the docking of small molecule ligands into protein structures, simulating cases where the real binding sites are unknown. The resulting approach consists of a few independent docking runs carried out on small boxes, centered on the predicted binding sites, as opposed to one larger blind docking run that covers the complete protein structure. The focused and blind approaches were compared using a set of 77 known protein-ligand complexes and 19 ligand-free structures. The focused approach is shown to: (1) identify the correct binding site more frequently than blind docking; (2) produce more accurate docking poses for the ligand; (3) require less computational ti

SUBMITTER: Ghersi D 

PROVIDER: S-EPMC2610246 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature