A Branch and Bound Algorithm for Matching Protein Structures

Authors:
Janez Konc;Dušanka Janežič
Affiliations:
National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia;National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
Venue:
ICANNGA '07 Proceedings of the 8th international conference on Adaptive and Natural Computing Algorithms, Part II
Year:
2007

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Abstract

An efficient branch and bound algorithm for matching protein structures has been developed. The compared protein structures are represented as graphs and a product graph of these graphs is calculated. The resulting product graph is then the input to our algorithm. A maximum clique in the product graph corresponds to the maximum common substructure in the original graphs. Our algorithm, which gives an approximate solution to the maximum clique problem, is compared with exact algorithms commonly used in bioinformatics for protein structural comparisons. The computational results indicate that the new algorithm permits an efficient protein similarity calculation used for protein structure analysis and protein classification.