title: An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins.
abstract: A computer program system was developed to predict carbohydrate-binding sites on three-dimensional (3D) protein structures. The programs search for binding sites by referring to the empirical rules derived from the known 3D structures of carbohydrate-protein complexes. A total of 80 non-redundant carbohydrate-protein complex structures were selected from the Protein Data Bank for the empirical rule construction. The performance of the prediction system was tested on 50 known complex structures to determine whether the system could detect the known binding sites. The known monosaccharide-binding sites were detected among the best three predictions in 59% of the cases, which covered 69% of the polysaccharide-binding sites in the target proteins, when the performance was evaluated by the overlap between residue patches of predicted and known binding sites.
authors.affiliation: Department of Biotechnology and Biomaterial Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.
authors.forename: Clara
authors.initials: C
authors.lastname: Shionyu-Mitsuyama
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Shirai
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Ishida
authors.forename: Takashi
authors.initials: T
authors.lastname: Yamane
mesh_terms: D000818:Animals; D001665:Binding Sites; D050260:Carbohydrate Metabolism; D030562:Databases, Protein; D006801:Humans; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins