Protein structure alignment using maximum cliques and local search
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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.
AI 2007: Advances in Artificial Intelligence
Copyright 2007 Springer. The original publication is available at www.springerlink.com This is the author-manuscript version of this paper. Reproduced in accordance with the copyright policy of the publisher.