title: Similarity searching in databases of three-dimensional molecules and macromolecules.
abstract: This paper discusses algorithmic techniques for measuring the degree of similarity between pairs of three-dimensional (3-D) chemical molecules represented by interatomic distance matrices. A comparison of four methods for the calculation of 3-D structural similarity suggests that the most effective one is a procedure that identifies pairs of atoms, one from each of the molecules that are being compared, that lie at the center of geometrically-related volumes of 3-D space. This atom mapping method enables the calculation of a wide range of types of intermolecular similarity coefficient, including measures that are based on physicochemical data. Massively-parallel implementations of the method are discussed, using the AMT Distributed Array Processor, that achieve a substantial increase in performance when compared with a sequential implementation on a UNIX workstation. Current work involves the use of angular information and the extension of the method to field-based similarity searching. Similarity searching in 3-D macromolecules is effected by the use of a maximal common subgraph (MCS) isomorphism algorithm with a novel, graph-based representation of the tertiary structures of proteins. This algorithm is being used to identify similarities between the 3-D structures of proteins in the Brookhaven Protein Data Bank; its use is exemplified by searches involving the NAD-binding fold motif.
authors: Department of Information Studies, Krebs Institute for Biomolecular Research, University of Sheffield, England.
authors: P J
authors: PJ
authors: Artymiuk
authors: P A
authors: PA
authors: Bath
authors: H M
authors: HM
authors: Grindley
authors: C A
authors: CA
authors: Pepperrell
authors: A R
authors: AR
authors: Poirrette
authors: D W
authors: DW
authors: Rice
authors: D A
authors: DA
authors: Thorner
authors: D J
authors: DJ
authors: Wild
authors: P
authors: P
authors: Willett
authors: F H
authors: FH
authors: Allen
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D016208:Databases, Factual; D046911:Macromolecular Substances; D015394:Molecular Structure; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013329:Structure-Activity Relationship
chemical_list: D046911:Macromolecular Substances; D011506:Proteins