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Similarity searching in databases of three-dimensional molecules and macromolecules

Artymiuk, P.J., Bath, P.A., Grindley, H.M., Pepperrell, C.A., Poirrette, A.R., Rice, D.W., Thorner, D.A., Wild, D.J., Willett, P., Allen, F.H. and Taylor, R. (1992) Similarity searching in databases of three-dimensional molecules and macromolecules. Journal of Chemical Information and Computer Sciences, 32 (6). pp. 617-630. ISSN 0095-2338

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This paper discusses algorithmic techniques for measuring the degree of similarity between pairs of threedimensional (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.

Item Type: Article
Institution: The University of Sheffield
Academic Units: The University of Sheffield > Faculty of Social Sciences (Sheffield) > Information School (Sheffield)
Depositing User: Information Studies
Date Deposited: 17 Aug 2009 10:55
Last Modified: 17 Aug 2009 10:55
Published Version: http://dx.doi.org/10.1021/ci00010a007
Status: Published
Identification Number: 10.1021/ci00010a007
URI: http://eprints.whiterose.ac.uk/id/eprint/9158

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