title: Fast screening of protein surfaces using geometric invariant fingerprints.
abstract: We develop a rapid and efficient method for the comparison of protein local surface similarities using geometric invariants (fingerprints). By combining fast fingerprint comparison with explicit alignment, we successfully screen the entire Protein Data Bank for proteins that possess local surface similarities. Our method is independent of sequence and fold similarities, and has potential application to protein structure annotation and protein-protein interface design.
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Genetics Medicine, 120 Mason Farm Road, Chapel Hill, NC 27599-7260, USA.
authors.forename: Shuangye
authors.initials: S
authors.lastname: Yin
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Proctor
authors.forename: Alexey A
authors.initials: AA
authors.lastname: Lugovskoy
authors.forename: Nikolay V
authors.initials: NV
authors.lastname: Dokholyan
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D008958:Models, Molecular; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry*; D040681:Structural Homology, Protein; D013499:Surface Properties
chemical_list: D011506:Proteins