title: Searching for patterns of amino acids in 3D protein structures.
abstract: This paper describes the program ASSAM, which has been developed to search for patterns of amino acid side-chains in the 3D structures in the Protein Data Bank. ASSAM represents an amino acid by a vector drawn from the main chain towards the functional part of the amino acid and then computes a graph representation of a protein in which the individual side-chain vectors are the nodes and the intervector distances are the edges. The presence of a query pattern in a Protein Data Bank structure can then be searched for by means of a subgraph isomorphism algorithm. Recent enhancements to ASSAM allow searches to include the following: the main-chain structure in addition to the side-chains; the secondary structure and solvent accessibility of side-chains; allowable distances from a known binding-site; disulfide bridges; and improved generic and wild-card queries. The effectiveness of these approaches is demonstrated by extensive searches of the Protein Data Bank for typical 3D query patterns.
authors.affiliation: Krebs Institute for Biomolecular Research and Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
authors.forename: Ruth V
authors.initials: RV
authors.lastname: Spriggs
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Artymiuk
authors.forename: Peter
authors.initials: P
authors.lastname: Willett
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D001665:Binding Sites; D030562:Databases, Protein; D004220:Disulfides / Q000737:chemistry; D016247:Information Storage and Retrieval; D008958:Models, Molecular; D010363:Pattern Recognition, Automated; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012697:Serine Endopeptidases / Q000737:chemistry / Q000378:metabolism; D012984:Software; D012997:Solvents
chemical_list: D000596:Amino Acids; D004220:Disulfides; D011506:Proteins; D012997:Solvents; D012697:Serine Endopeptidases