Combination of generalized-ensemble algorithms and one-dimensional reference interaction site model theory

A. Mitsutake, M. Kinoshita, F. Hirata, Y. Okamoto

Research output: Contribution to journalReview article

Abstract

The article reports an attempt to study the protein folding problem by generalized-ensemble Monte Carlo simulations with reference interaction site model theory. Generalized-ensemble algorithms greatly enhance the configurational space sampling in computer simulations. The reference interaction site model theory treats solvent effects with solvent molecular shape and estimate solvation free energy around proteins. We have developed simulation algorithms which combine generalized-ensemble algorithms and one-dimensional reference interaction site model theory. This treatment can also use a simulation with three-dimensional reference interaction site model theory. In this review, we describe the methods and present the results of these simulations for a peptide.

Original languageEnglish
Pages (from-to)495-508
Number of pages14
JournalCondensed Matter Physics
Volume10
Issue number4
DOIs
Publication statusPublished - 2007 Jan 1

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Keywords

  • Generalized-ensemble algorithm
  • Monte Carlo
  • Multicanonical algorithm
  • Protein folding
  • RISM
  • Replica-exchange method

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Physics and Astronomy (miscellaneous)

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