Name
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. |
Year | DOI | Venue |
|---|---|---|
1992 | 10.1021/ci00010a007 | JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES |
Keywords | Field | DocType |
similarity search,three dimensional | Three-dimensional space,Similitude,Combinatorics,Distance matrices in phylogeny,Macromolecule,Computational chemistry,Algorithm,Structural similarity,Isomorphism,Protein Data Bank,Intermolecular force,Mathematics | Journal |
Volume | Issue | ISSN |
32 | 6 | 0095-2338 |
Citations | PageRank | References |
10 | 1.33 | 0 |
Authors | ||
9 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Peter J. Artymiuk | 1 | 203 | 19.62 |
| Peter A. Bath | 2 | 183 | 27.79 |
| Helen M. Grindley | 3 | 23 | 4.59 |
| Catherine A. Pepperrell | 4 | 26 | 3.26 |
| Andrew R. Poirrette | 5 | 50 | 9.21 |
| David W. Rice | 6 | 41 | 7.33 |
| David A. Thorner | 7 | 56 | 12.13 |
| David J. Wild | 8 | 416 | 30.58 |
| PETER WILLETT | 9 | 3421 | 592.93 |