title: Evaluation of the searching abilities of HBOP and HBSITE for binding pocket detection.
abstract: We evaluated the pocket-searching abilities of the computer programs HBOP and HBSITE, in which hydrophobic potentials calculated on grid points generated around a protein function as an indicator of the pocket-like property-using a test set of 458 experimentally observed structures of protein-ligand complexes. The results were compared with those obtained using the alternative algorithms PASS and SiteID, which only consider geometric properties, and Q-SiteFinder, which considers not only geometry but also physicochemical properties. The comparison revealed that HBOP and HBSITE could detect experimentally observed ligand-binding pockets for more test complexes than PASS and SiteID. In addition, the success rate of HBOP for detecting binding pockets was higher than that of Q-SiteFinder, and that of HBSITE was comparable with that of Q-SiteFinder. Results of tests for ligand-unbound state proteins indicated that HBSITE was more appropriate than Q-SiteFinder for pocket searches of ligand-unbound proteins, and HBSITE was more robust than Q-SiteFinder against structural differences between ligand-bound and -unbound state proteins.
authors.affiliation: Discovery Laboratories, Toyama Chemical Co., Ltd., 2-4-1 Shimookui, Toyama 930-8508, Japan. oda@tohoku-pharm.ac.jp
authors.forename: Akifumi
authors.initials: A
authors.lastname: Oda
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Yamaotsu
authors.forename: Shuichi
authors.initials: S
authors.lastname: Hirono
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D030562:Databases, Protein; D008024:Ligands; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins