HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) All Versions of this Article: T200001-MCP200v1 1/4/334    most recent Submit a response Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Request Permissions Glossary Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Taylor, W. R. Search for Related Content PubMed PubMed Citation Articles by Taylor, W. R. Social Bookmarking                      What's this?

Molecular & Cellular Proteomics 1:334-339, 2002.
© 2002 by The American Society for Biochemistry and Molecular Biology, Inc.

---

Technology

Protein Structure Comparison Using Bipartite Graph Matching and Its Application to Protein Structure Classification ^*

William R. Taylor

From the Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom

A measure of protein structure similarity is calculated from the matching of pairs of secondary structure elements between two proteins. The interaction of each pair was estimated from their axial line segments and combined with other geometric features to produce an optimal discrimination between intrafamily and interfamily relationships. The matching used a fast bipartite graph-matching algorithm that avoids the computational complexity of searching for the full subgraph isomorphism between the two sets of interactions. The main algorithm used was the "stable marriage" algorithm, which works on the ranked "preferences" of one interaction for another. The method takes 1/10 of a second for a typical comparison making it suitable as a fast pre-filter for slower, more exhaustive approaches. An application to protein structure classification is described.

CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				L. O. Johannissen and W. R. Taylor Protein fold comparison by the alignment of topological strings Protein Eng. Des. Sel., December 1, 2003; 16(12): 949 - 955. [Abstract] [Full Text] [PDF]