title: [Development and validation of programs for ligand-binding-pocket search].
abstract: Searching for the ligand-binding pockets of proteins plays an important role in structure-based drug design (SBDD), which is based on knowledge of the three-dimensional structures of target proteins. In SBDD, small molecules that can interact with the target protein are designed. SBDD methods require the identification of ligand-binding pockets, in which ligand molecules interact with protein atoms. The computer programs for the detection of ligand-binding pockets are categorized into two types: one is programs using only geometric properties; and the other is programs using the physicochemical properties of proteins as well as geometry. This paper describes the development and evaluation of a program for ligand-binding pocket search. The program HBOP (Hydropho Bicity On a Protein) searches for ligand-binding pockets using hydrophobic potentials derived from experimentally determined functions. This is based on the fact that hydrophobicity plays a significant role in protein-ligand binding. The results of evaluation indicate that programs using physicochemical properties can discover actual ligand-binding pockets more efficiently than those using only geometric properties.
authors.affiliation: Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, Sendai, Japan. oda@tohoku-pharm.ac.jp
authors.forename: Akifumi
authors.initials: A
authors.lastname: Oda
mesh_terms: D001665:Binding Sites; D001690:Biological Science Disciplines / Q000379:methods*; D002627:Chemistry, Physical; D019295:Computational Biology / Q000379:methods*; D015195:Drug Design; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D046912:Multiprotein Complexes; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D008024:Ligands; D046912:Multiprotein Complexes; D011506:Proteins