Please use this identifier to cite or link to this item: http://hdl.handle.net/10525/1583

 Title: Solving Maximum Clique Problem for Protein Structure Similarity Authors: Malod-Dognin, NoëlAndonov, RumenYanev, Nicola Keywords: Protein Structure ComparisonMaximum CliqueK-Partite GraphsInteger ProgrammingBranch and Bound Issue Date: 2010 Publisher: Institute of Mathematics and Informatics Bulgarian Academy of Sciences Citation: Serdica Journal of Computing, Vol. 4, No 1, (2010), 93p-100p Abstract: Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum weighted clique problems in specific k-partite graphs, referred here as alignment graphs. In this paper we present both a new integer programming formulation for solving such clique problems and a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches have been integrated in VAST, a software for aligning protein 3D structures largely used in the National Center for Biotechnology Information, an original clique solver which uses the well known Bron and Kerbosch algorithm (BK). Our computational results on real protein alignment instances show that our branch and bound algorithm is up to 116 times faster than BK. URI: http://hdl.handle.net/10525/1583 ISSN: 1312-6555 Appears in Collections: Volume 4 Number 1

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