Protein structure alignment using maximum cliques and local search
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.
Conference Title
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume
4830 LNAI
Copyright Statement
© 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.