Multiobjectivizing the HP Model for Protein Structure Prediction

Abstract. The hydrophobic-polar (HP) model for protein structure preabstracts the fact that hydrophobic interactions are a dominant force in the protein folding process. This model represents a hard combinatorial optimization problem, which has been widely addressed using evolutionary algorithms and other metaheuristics. In this paper, the multiobjectivization of the HP model is proposed. This originally singleobjective problem is restated as a multiobjective one by decomposing the conventional objective function into two independent objectives. By using different evolutionary algorithms and a large set of test cases, the new alternative formulation was compared against the conventional singleobjective problem formulation. As a result, the proposed formulation increased the search performance of the implemented algorithms in most of the cases. Both two- and three-dimensional lattices are considered. To the best of authors’ knowledge, this is the first study where multiobjective opt...

• Type: Journal
• Year: 2012
• Where: EVOW
• Authors: Mario Garza-Fabre, Eduardo Rodriguez-Tello, Gregorio Toscano Pulido
• Keywords: Artificial Intelligence, Combinatorial Optimization Problem, Evolutionary Algorithms, EVOW 2012, Hp Model