PMID: 9541870May 16, 1998Paper

Pairwise and multiple identification of three-dimensional common substructures in proteins

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
V EscalierA Viari

Abstract

In this paper, we present an algorithm to find three-dimensional substructures common to two or more molecules. The basic algorithm is devoted to pairwise structural comparison. Given two sets of atomic coordinates, it finds the largest subsets of atoms which are "similar" in the sense that all internal distances are approximately conserved. The basic idea of the algorithm is to recursively build subsets of increasing sizes, combining two sets of size k to build a set of size k + 1. The algorithm can be used "as is" for small molecules or local parts of proteins (about 30 atoms). When a high number of atoms is involved, we use a two step procedure. First we look for common "local" fragments by using the previous algorithm, and then we gather these fragments by using a Branch and Bound technique. We also extend the basic algorithm to perform multiple comparisons, by using one of the structures as a reference point (pivot) to which all other structures are compared. The solution is the largest subsets of atoms common to the pivot and at least q other structures. Although both algorithms are theoretically exponential in the number of atoms, experiments performed on biological data and using realistic parameters show that the solut...Continue Reading

References

May 25, 1977·Journal of Molecular Biology·F C BernsteinM Tasumi
Jan 1, 1994·Critical Reviews in Biochemistry and Molecular Biology·M S JohnsonT L Blundell

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Citations

Jul 9, 1998·Protein Science : a Publication of the Protein Society·V MikolC K Carlow
Jan 12, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·I EidhammerW R Taylor
Jan 6, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Nadia PisantiJoel Pothier
Aug 13, 2009·BMC Bioinformatics·Flavien QuintusPierre Tuffery
Mar 29, 2014·BMC Bioinformatics·Brett HansonPaul A Craig
Dec 21, 2004·Proteins·Jianhua Zhu, Zhiping Weng
Dec 24, 2004·Proteins·Jordi Mestres
Jul 29, 2005·Proteins·Mathilde CarpentierJoël Pothier
Oct 24, 2003·Protein Science : a Publication of the Protein Society·Oranit DrorHaim J Wolfson
Nov 16, 2007·Proteins·M TyagiB Offmann
Dec 15, 2010·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Alexandra Veyrac, Julie Bakker

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