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Protein Structure Prediction in Lattice Models with Particle Swarm Optimization

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Swarm Intelligence (ANTS 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6234))

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Abstract

The protein structure prediction problem consists in finding good computational algorithms for prediction of protein native states. This paper applies the Particle Swarm Optimization (PSO) algorithm to predict the tertiary structure of proteins in lattice models. We propose a novel discrete PSO variant designed for lattice-based protein folding models. We present three lattice based models and two folding encodings, which are tested in different combinations on six proteins. The results indicate that the new algorithm performs very efficient and finds very good proteins conformations.

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Authors and Affiliations

  1. Faculty of Computer Science, “Al. I. Cuza” University, Iasi, Romania

    Andrei Băutu & Henri Luchian

Authors
  1. Andrei Băutu
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  2. Henri Luchian
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Editor information

Editors and Affiliations

  1. IRIDIA, CoDE, Université Libre de Bruxelles, Brussels, Belgium

    Marco Dorigo

  2. IRIDIA, CoDE, Université Libre de Bruxelles, Av. F. Roosevelt 50, CP 194/6, 1050, Brussels, Belgium

    Mauro Birattari

  3. ’Dalla Molle’ Institute for Artificial Intelligence (IDSIA), Galleria 2, 6928, Manno-Lugano, Switzerland

    Gianni A. Di Caro

  4. Complex Systems Institute, Paris-Ile-de-France, CREA, Ecole Polytechnique & CNRS, 57-59, rue Lhomond, 75005, Paris, France

    René Doursat

  5. Department of Computer Science, University of Pretoria, 0002, P.O. Box, Pretoria, South Africa

    Andries P. Engelbrecht

  6. EPFL, Laboratory of Intelligent Systems, Lausanne, Switzerland

    Dario Floreano

  7. Istituto Dalle Molle di Studi sull’Intelligenza Artificiale (IDSIA), Lugano, Switzerland

    Luca Maria Gambardella

  8. Department of Automatic Control and Systems Engineering, The University of Sheffield, Mappin Street, S1 3JD, Sheffield, UK

    Roderich Groß

  9. KOVAN Research Lab., Department of Computer Engineering, Middle East Technical University, Inonu Bulvari, 06531, Ankara, Turkey

    Erol Şahin

  10. Department of Bioengineering, Binghamton University, State University of New York, 13902-6000, Binghamton NY, USA

    Hiroki Sayama

  11. IRIDIA, CoDE, Université Libre de Bruxelles, Avenue F. Roosevelt 50, CP 194/6, 1050, Brussels, Belgium

    Thomas Stützle

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Băutu, A., Luchian, H. (2010). Protein Structure Prediction in Lattice Models with Particle Swarm Optimization. In: Dorigo, M., et al. Swarm Intelligence. ANTS 2010. Lecture Notes in Computer Science, vol 6234. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15461-4_51

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  • DOI: https://doi.org/10.1007/978-3-642-15461-4_51

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-15460-7

  • Online ISBN: 978-3-642-15461-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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