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Multiobjectivizing the HP Model for Protein Structure Prediction

  • Conference paper
Evolutionary Computation in Combinatorial Optimization (EvoCOP 2012)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7245))

Abstract

The hydrophobic-polar (HP) model for protein structure prediction abstracts 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 single-objective 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 single-objective 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 optimization methods are used for solving the HP model.

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Authors and Affiliations

  1. Information Technology Laboratory, CINVESTAV-Tamaulipas, Parque Científico y Tecnológico TECNOTAM, Km. 5.5 carretera Cd. Victoria-Soto La Marina, Cd. Victoria, Tamaulipas, 87130, México

    Mario Garza-Fabre, Eduardo Rodriguez-Tello & Gregorio Toscano-Pulido

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  1. Mario Garza-Fabre
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  2. Eduardo Rodriguez-Tello
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  3. Gregorio Toscano-Pulido
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Editors and Affiliations

  1. Faculty of Angers, University of Angers, 2, Boulevard Lavoisier, 49045, Angers Cedex 01, France

    Jin-Kao Hao

  2. Department of Computer Science, University of Leipzig, Johannisgasse 26, 04103, Leipzig, Germany

    Martin Middendorf

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Garza-Fabre, M., Rodriguez-Tello, E., Toscano-Pulido, G. (2012). Multiobjectivizing the HP Model for Protein Structure Prediction. In: Hao, JK., Middendorf, M. (eds) Evolutionary Computation in Combinatorial Optimization. EvoCOP 2012. Lecture Notes in Computer Science, vol 7245. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29124-1_16

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  • DOI: https://doi.org/10.1007/978-3-642-29124-1_16

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-29123-4

  • Online ISBN: 978-3-642-29124-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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