Calculation of Three-Dimensional Structural Similarity

  • Catherine A. Pepperrell
  • Peter Willett
Conference paper


This poster reports work to date on a project to evaluate techniques for measuring the degree of similarity between pairs of 3-D chemical structures represented by interatomic distance matrices. The four techniques that have been tested use the distance information in very different ways and have very different computational requirements. Preliminary experiments with two small data-sets, 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.


Atom Mapping Molecular Similarity Polycyclic Hydrocarbon Distance Match Tanimoto Coefficient 
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Copyright information

© Springer-Verlag Berlin Heidelberg 1993

Authors and Affiliations

  • Catherine A. Pepperrell
    • 1
  • Peter Willett
    • 1
  1. 1.Department of Information StudiesUniversity of SheffieldSheffieldEngland

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