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Originally published In Press as doi:10.1074/mcp.T200001-MCP200 on March 4, 2002.
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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{ddagger}

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.

{ddagger} To whom correspondence should be addressed. Tel.: 44-02089138552; Fax: 44-02089138545; E-mail: wtaylor{at}nimr.mrc.ac.uk


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Copyright © 2002 by the American Society for Biochemistry and Molecular Biology.