Protein structure alignment using maximum cliques and local search

Authors:
Wayne Pullan
Affiliations:
School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
Venue:
AI'07 Proceedings of the 20th Australian joint conference on Advances in artificial intelligence
Year:
2007

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Abstract

The protein structure alignment problem addresses the question of measuring the degree of similarity, in three-dimensional structure, of two proteins. The representation of each protein using a simple contact map allows the correspondence graph for the protein pair to be generated and the maximum clique within this graph provides a measure of the structural similarity between the two proteins. This study uses a recently developed maximum clique algorithm, Phased Local Search (PLS), to locate the maximum cliques within correspondence graphs.