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 journalArticle

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
Publication statusPublished - 2007

Fingerprint

simulation
interactions
proteins
folding
peptides
solvation
computerized simulation
sampling
free energy
estimates

Keywords

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

ASJC Scopus subject areas

  • Physics and Astronomy (miscellaneous)
  • Condensed Matter Physics

Cite this

Combination of generalized-ensemble algorithms and one-dimensional reference interaction site model theory. / Mitsutake, A.; Kinoshita, M.; Hirata, F.; Okamoto, Y.

In: Condensed Matter Physics, Vol. 10, No. 4, 2007, p. 495-508.

Research output: Contribution to journalArticle

Mitsutake, A, Kinoshita, M, Hirata, F & Okamoto, Y 2007, 'Combination of generalized-ensemble algorithms and one-dimensional reference interaction site model theory', Condensed Matter Physics, vol. 10, no. 4, pp. 495-508.
Mitsutake, A. ; Kinoshita, M. ; Hirata, F. ; Okamoto, Y. / Combination of generalized-ensemble algorithms and one-dimensional reference interaction site model theory. In: Condensed Matter Physics. 2007 ; Vol. 10, No. 4. pp. 495-508.
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