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Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms

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Computational Methods for Macromolecules: Challenges and Applications

Part of the book series: Lecture Notes in Computational Science and Engineering ((LNCSE,volume 24))

Abstract

We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchange method; the latter is also referred to as parallel tempering. We present a new generalized-ensemble algorithm that combines the merits of the two methods; it is referred to as the replica-exchange multicanonical algorithm. We also give a multidimensional extension of the replica-exchange method. Its realization as an umbrella sampling method, which we refer to as the replica-exchange umbrella sampling, is a powerful algorithm that can give free energy in wide reaction coordinate space.

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Authors and Affiliations

  1. Department of Theoretical Studies, Institute for Molecular Science, Okazaki, Aichi, 444-8585, Japan

    Yuji Sugita & Yuko Okamoto

  2. Department of Functional Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi, 444-8585, Japan

    Yuji Sugita & Yuko Okamoto

Authors
  1. Yuji Sugita
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  2. Yuko Okamoto
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Editors and Affiliations

  1. Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY, 10012, USA

    Tamar Schlick  & Hin Hark Gan  & 

  2. Howard Hughes Medical Institute, 251 Mercer Street, New York, NY, 10012, USA

    Tamar Schlick  & Hin Hark Gan  & 

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© 2002 Springer-Verlag Berlin Heidelberg

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Sugita, Y., Okamoto, Y. (2002). Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms. In: Schlick, T., Gan, H.H. (eds) Computational Methods for Macromolecules: Challenges and Applications. Lecture Notes in Computational Science and Engineering, vol 24. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-56080-4_13

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  • DOI: https://doi.org/10.1007/978-3-642-56080-4_13

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-43756-7

  • Online ISBN: 978-3-642-56080-4

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