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A Replica Exchange Monte Carlo Algorithm for the Optimization of Secondary Structure Packing in Proteins

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Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6023))

Abstract

We approach the problem of packing secondary structure fragments into low energy conformations with a local search optimization algorithm. Protein conformations are represented in a simplified off-lattice model. In that model we propose a move set that transforms a protein conformation into another in order to enable the use of local search algorithms for protein folding simulations and conformational search. The energy minimization problem behind protein folding is adapted to our model. Special care has been taken so that amino acids in a conformation do not overlap. The constraint of producing an overlap-free conformation can be seen as a objective that conflicts with the energy minimization. Thus, we approach protein folding as a two-objective problem. We employ a replica exchange Monte Carlo algorithm in combination to the proposed move set. The algorithm deals with the energy minimization problem while maintaining overlap-free conformations. Initial conformations incorporate experimentally determined secondary structure, which is preserved throughout the execution of local search. Our method produced conformations with a minimum RMSD of alpha-carbon atoms in the range of 4.71Å to 6.82Å for all benchmarks apart from one for which the value was 9.68Å.

Research partially supported by EPSRC Grant No. EP/D062012/1.

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Authors and Affiliations

  1. Department of Computer Science, King’s College London, The Strand, London, WC2R 2LS, United Kingdom

    Leonidas Kapsokalivas & Kathleen Steinhöfel

Authors
  1. Leonidas Kapsokalivas
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  2. Kathleen Steinhöfel
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Editor information

Editors and Affiliations

  1. Institute for High-Performance Computing and Networking (ICAR), Italian National Research Council (CNR), Via P. Bucci 41C, 87036, Rende, (CS), Italy

    Clara Pizzuti

  2. Department of Molecular Physiology and Biophysics, Vanderbilt University, Center for Human Genetics Research, 519 Light Hall, 37232, Nashville, TN, USA

    Marylyn D. Ritchie

  3. Department of Animal Production Epidemiology and Ecology, University of Torino, Molecular Biotechnology Center, Via Leonardo da Vinci 44, 10095, Grugliasco, (TO), Italy

    Mario Giacobini

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Kapsokalivas, L., Steinhöfel, K. (2010). A Replica Exchange Monte Carlo Algorithm for the Optimization of Secondary Structure Packing in Proteins. In: Pizzuti, C., Ritchie, M.D., Giacobini, M. (eds) Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics. EvoBIO 2010. Lecture Notes in Computer Science, vol 6023. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-12211-8_13

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  • DOI: https://doi.org/10.1007/978-3-642-12211-8_13

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-12210-1

  • Online ISBN: 978-3-642-12211-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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