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An Enhanced Genetic Algorithm for Protein Structure Prediction Using the 2D Hydrophobic-Polar Model

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Artificial Evolution (EA 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3871))

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Abstract

This paper presents an enhanced genetic algorithm for the protein structure prediction problem. A new fitness function, that uses the concept of radius of gyration, is proposed. Also, a novel operator called partial optimization, together with different strategies for performance improvement, are described. Tests were done with five different amino acid chains from 20 to 85 residues long and better results were obtained, when compared with those in the current literature. Results are promising and suggest the suitability of the proposed method for protein structure prediction using the 2D HP model. Further experiments shall be done with longer amino acid chains as well as with real-world proteins.

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Authors and Affiliations

  1. Bioinformatics Lab. (CPGEI), Centro Federal de Educação Tecnológica do Paraná, Av. 7 de setembro, 3165 – 80230-901, Curitiba, Brazil

    Heitor S. Lopes & Marcos P. Scapin

Authors
  1. Heitor S. Lopes
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  2. Marcos P. Scapin
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Editor information

Editors and Affiliations

  1. INRIA Lille - Nord Europe Research Centre, Parc Scientifique de la Haute Borne, 59650, Villeneuve d’Ascq, France

    El-Ghazali Talbi

  2. UMR-CNRS 6632, Université de Provence, 39 rue F. Joliot-Curie, 13453, Marseille cedex 13, France

    Pierre Liardet

  3. Université Louis Pasteur, LSIIT, FDBT, Pôle API, F-67400, Illkirch, France

    Pierre Collet

  4. INRIA Saclay - Ile-de-France, Parc Orsay Université, 4, rue Jacques Monod, 91893, ORSAY Cedex, France

    Evelyne Lutton

  5. TAO, INRIA Saclay & LRI (UMR CNRS 8623), Bât 490, Université Paris-Sud, 91405, Orsay Cedex, France

    Marc Schoenauer

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© 2006 Springer-Verlag Berlin Heidelberg

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Lopes, H.S., Scapin, M.P. (2006). An Enhanced Genetic Algorithm for Protein Structure Prediction Using the 2D Hydrophobic-Polar Model. In: Talbi, EG., Liardet, P., Collet, P., Lutton, E., Schoenauer, M. (eds) Artificial Evolution. EA 2005. Lecture Notes in Computer Science, vol 3871. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11740698_21

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  • DOI: https://doi.org/10.1007/11740698_21

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-33589-4

  • Online ISBN: 978-3-540-33590-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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