Ant Colony Optimization for Construction of Common Pattern of the Protein Motifs

In this work is presented an approach for the construction of common patterns of the protein motifs of the amyloid protein motifs, extracted from the database AMYPdb, denoted as regular expressions using the rules PROSITE. Our task is to analyze a set of possible motifs and to detect if similarity exists between them, in order to construct a general motif. The Ant Colony Optimization Model uses an algorithm of combinatorial optimization based on Ant Colonies. It uses the amino acids of the first motif to construct the graph where the ants will walk. Then, the graph is crossed by the ants according to the path of the second motif, used by a transition function that promove to flow the path between similars amino acids. The ants when walking leave pheromone in the nodes, in a way that at the end several have a lot of or little pheromone. Finally the graph is crossed again to construct the resultant regular expression composed by the nodes with much pheromone.