Research Papers

Journal of Computer-Aided Molecular Design

, Volume 5, Issue 5, pp 455-474

First online:

Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances

  • Catherine A. PepperrellAffiliated withDepartment of Information Studies, University of Sheffield
  • , Peter WillettAffiliated withDepartment of Information Studies, University of Sheffield

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This paper reports a comparison of several methods for measuring the degree of similarity between pairs of 3-D chemical structures that are represented by inter-atomic distance matrices. The methods that have been tested use the distance information in very different ways and have very different computational requirements. Experiments with 10 small datasets, for which both structural and biological activity data are available, suggest that the most cost-effective technique is based on a mapping procedure that tries to match pairs of atoms, one from each of the molecules that are being compared, that have neighbouring atoms at approximately the same distances.

Key words

Inter-atomic distances Similarity searching Structure matching algorithms Three-dimensional chemical structure databases