Journal of Computer-Aided Molecular Design

, Volume 6, Issue 6, pp 607–628

A fast and efficient method for 2D and 3D molecular shape description

  • Guy W. Bemis
  • Irwin D. Kuntz
Research Papers

DOI: 10.1007/BF00126218

Cite this article as:
Bemis, G.W. & Kuntz, I.D. J Computer-Aided Mol Des (1992) 6: 607. doi:10.1007/BF00126218


A new formalism for molecular shape description is described. The formalism, based on considering each molecule as a collection of its 3-atom submolecules, is applied to both the graph theory and geometrical coordinate representations of molecules. The timing results for shape description of several databases indicate that this new method is applicable to large databases. Furthermore, results from clustering a small database show good agreement with clustering results obtained by a distance-matching algorithm.

Key words

Molecular similarityDatabase clusteringMolecular comparison

Copyright information

© ESCOM Science Publishers B.V 1992

Authors and Affiliations

  • Guy W. Bemis
    • 1
  • Irwin D. Kuntz
    • 1
  1. 1.Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoU.S.A.