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Generalized-Ensemble Algorithms for Studying Protein Folding

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Book cover Water and Biomolecules

Part of the book series: Biological and Medical Physics, Biomedical ((BIOMEDICAL))

Abstract

Conventional simulations of biomolecular systems will get trapped in states of local-minimum energy. A simulation in generalized ensemble overcomes this difficulty by performing a random walk in potential energy space and other parameter space. From only one simulation run, one can obtain accurate canonical-ensemble averages of physical quantities as functions of temperature and other parameters of the sytem by the single-histogram and/or multiple-histogram reweighting techniques. In this article, we review the generalized-ensemble algorithms. Two well-known methods, namely, multicanonical algorithm and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present further extensions of the above two methods.

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  1. Department of Physics Nagoya University, Nagoya Aichi, 464-8602, Japan

    Y. Okamoto

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  1. Y. Okamoto
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Editors and Affiliations

  1. Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan

    Kunihiro Kuwajima

  2. Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan

    Yuji Goto

  3. Institute for Molecular Science Department for Theoretical and Computational Molecular Science, National Institutes of Natural Sciences, 38 Nishigo-Naka, Myodaiji, Okazaki, 444-8585, Japan

    Fumio Hirata

  4. Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-6 Takayama, Ikoma, Nara, 630-0192, Japan

    Mikio Kataoka

  5. Graduate School of Science, Department of Chemistry, Kyoto University, Oiwakecho, Kitashirakawa, Kyoto, 606-8502, Japan

    Masahide Terazima

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© 2009 Springer-Verlag Berlin Heidelberg

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Okamoto, Y. (2009). Generalized-Ensemble Algorithms for Studying Protein Folding. In: Kuwajima, K., Goto, Y., Hirata, F., Kataoka, M., Terazima, M. (eds) Water and Biomolecules. Biological and Medical Physics, Biomedical . Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88787-4_4

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