PMID: 9524934Aug 1, 1997Paper

Clique-detection algorithms for matching three-dimensional molecular structures

Journal of Molecular Graphics & Modelling
E J GardinerPeter Willett

Abstract

The representation of chemical and biological molecules by means of graphs permits the use of a maximum common subgraph (MCS) isomorphism algorithm to identify the structural relationships existing between pairs of such molecular graphs. Clique detection provides an efficient way of implementing MCS detection, and this article reports a comparison of several different clique-detection algorithms when used for this purpose. Experiments with both small molecules and proteins demonstrate that the most efficient of these particular applications, which typically involve correspondence graphs with low edge densities, is the algorithm described by Carraghan and Pardalos. This is shown to be two to three times faster than the Bron-Kerbosch algorithm that has been used previously for MCS applications in chemistry and biology. However, the latter algorithm enables all substructures common to a pair of molecules to be identified, and not just the largest ones, as with the other algorithms considered here. The two algorithms can usefully be combined to increase the efficiency of database-searching systems that use the MCS as a measure of structural similarity.

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Citations

Jun 23, 2009·Journal of Computer-aided Molecular Design·Deepak BandyopadhyayAlexander Tropsha
Dec 3, 1999·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·P Willett
Feb 7, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Lu HeChris Bailey-Kellogg
Jul 5, 2008·Briefings in Functional Genomics & Proteomics·Pier Federico Gherardini, Manuela Helmer-Citterich
Aug 22, 2009·Bioinformatics·M J L de GrootD de Ridder
Dec 14, 1999·Protein Science : a Publication of the Protein Society·K S Makarova, N V Grishin
Aug 29, 2013·Evidence-based Complementary and Alternative Medicine : ECAM·Ming YangGuang Ji
Apr 13, 2000·Journal of Chemical Information and Computer Sciences·A TingS Green
May 30, 2007·British Journal of Pharmacology·D Rognan
Mar 11, 2017·Journal of Chemical Information and Modeling·Inès RasoloheryFrédéric Guyon
Aug 20, 2003·Journal of Computational Chemistry·Richard D TaylorJonathan W Essex
Apr 23, 2005·Human Brain Mapping·Jack L LancasterPeter T Fox
May 28, 2019·Nucleic Acids Research·Julien ReyGautier Moroy
Dec 1, 2013·Molecular Informatics·Xavier Jalencas, Jordi Mestres
Nov 28, 2006·Journal of Chemical Information and Modeling·William Lingran Chen
Mar 26, 2003·Journal of Chemical Information and Computer Sciences·Nicholas RhodesChristine Humblet
Nov 17, 2009·Journal of Chemical Information and Modeling·Eleanor J GardinerValerie J Gillet
Jun 25, 2005·Journal of Medicinal Chemistry·Peter Willett

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