A new memetic algorithm for multiple graph alignment

Abstract

One of the main tasks of structural biology is comparing the structure of proteins. Comparisons of protein structure can determine their functional similarities. Multigraph alignment is a useful tool for identifying functional similarities based on structural analysis. This article proposes a new algorithm for aligning protein binding sites called ACOTS-MGA. This algorithm is based on the memetic scheme. It uses the ACO method to construct a set of solutions, then selects the best solution for implementing Tabu Search to improve the solution quality. Experimental results have shown that ACOTS-MGA outperforms state-of-the-art algorithms while producing alignments of better quality.KeywordsMultiple Graph Alignment, Tabu Search, Ant Colony Optimization, local search, memetic algorithm, SMMAS pheromone update rule, protein active sitesReferencesE. Todd, C. A. Orengo, and J. M. Thornton, “Evolution of function in protein superfamilies, from a structural perspective,” J. Mol. 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