title: Analysis and prediction of carbohydrate binding sites.
abstract: An analysis of the characteristic properties of sugar binding sites was performed on a set of 19 sugar binding proteins. For each site six parameters were evaluated: solvation potential, residue propensity, hydrophobicity, planarity, protrusion and relative accessible surface area. Three of the parameters were found to distinguish the observed sugar binding sites from the other surface patches. These parameters were then used to calculate the probability for a surface patch to be a carbohydrate binding site. The prediction was optimized on a set of 19 non-homologous carbohydrate binding structures and a test prediction was carried out on a set of 40 protein-carbohydrate complexes. The overall accuracy of prediction achieved was 65%. Results were in general better for carbohydrate-binding enzymes than for the lectins, with a rate of success of 87%.
authors.affiliation: Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.
authors.forename: C
authors.initials: C
authors.lastname: Taroni
authors.forename: S
authors.initials: S
authors.lastname: Jones
authors.forename: J M
authors.initials: JM
authors.lastname: Thornton
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D001185:Artificial Intelligence; D001665:Binding Sites; D050260:Carbohydrate Metabolism; D002241:Carbohydrates / Q000737:chemistry*; D016208:Databases, Factual; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry / Q000378:metabolism; D037102:Lectins / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008956:Models, Chemical; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D012997:Solvents / Q000494:pharmacology; D014961:X-Ray Diffraction
chemical_list: D000596:Amino Acids; D002241:Carbohydrates; D004798:Enzymes; D007140:Immunoglobulin Fab Fragments; D037102:Lectins; D008024:Ligands; D011506:Proteins; D012997:Solvents