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Similarity searching in files of three-dimensional chemical structures: Representation and searching of molecular electrostatic potentials using field-graphs

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Abstract

This paper reports a method for the identification of those molecules in a database of rigid 3D structures with molecular electrostatic potential (MEP) grids that are most similar to that of a user-defined target molecule. The most important features of an MEP grid are encoded in field-graphs, and a target molecule is matched against a database molecule by a comparison of the corresponding field-graphs. The matching is effected using a maximal common subgraph isomorphism algorithm, which provides an alignment of the target molecule's field- graph with those of each of the database molecules in turn. These alignments are used in the second stage of the search algorithm to calculate the intermolecular MEP similarities. Several different ways of generating field-graphs are evaluated, in terms of the effectiveness of the resulting similarity measures and of the associated computational costs. The most appropriate procedure has been implemented in an operational system that searches a corporate database, containing ca. 173,000 3D structures.

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Authors and Affiliations

  1. Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Sheffield, S10 2TN, U.K

    David A. Thorner, Peter Willett & P. Matthew Wright

  2. Zeneca Agrochemicals, Jealott's Hill Research Station, Bracknell, Berkshire, RG12 6EY, U.K.

    Robin Taylor

Authors
  1. David A. Thorner
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  2. Peter Willett
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  3. P. Matthew Wright
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  4. Robin Taylor
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Thorner, D.A., Willett, P., Wright, P.M. et al. Similarity searching in files of three-dimensional chemical structures: Representation and searching of molecular electrostatic potentials using field-graphs. J Comput Aided Mol Des 11, 163–174 (1997). https://doi.org/10.1023/A:1008034527445

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