title: AI-based algorithms for protein surface comparisons.
abstract: Many current methods for protein analysis depend on the detection of similarity in either the primary sequence, or the overall tertiary structure (the Calpha atoms of the protein backbone). These common sequences or structures may imply similar functional characteristics or active properties. Active sites and ligand binding sites usually occur on or near the surface of the protein; so similarly shaped surface regions could imply similar functions. We investigate various methods for describing the shape properties of protein surfaces and for comparing them. Our current work uses algorithms from computer vision to describe the protein surfaces, and methods from graph theory to compare the surface regions. Early results indicate that we can successfully match a family of related ligand binding sites, and find their similarly shaped surface regions. This method of surface analysis could be extended to help identify unknown surface regions for possible ligand binding or active sites.
authors.affiliation: School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
authors.forename: S J
authors.initials: SJ
authors.lastname: Pickering
authors.forename: A J
authors.initials: AJ
authors.lastname: Bulpitt
authors.forename: N
authors.initials: N
authors.lastname: Efford
authors.forename: N D
authors.initials: ND
authors.lastname: Gold
authors.forename: D R
authors.initials: DR
authors.lastname: Westhead
mesh_terms: D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D001665:Binding Sites; D024601:Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+) / Q000737:chemistry; D006736:Horses; D006801:Humans; D007894:Leishmania mexicana / Q000201:enzymology; D009243:NAD / Q000378:metabolism; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013499:Surface Properties
chemical_list: D011506:Proteins; D009243:NAD; D024601:Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+)