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 language | English |
|---|---|
| Pages (from-to) | 495-508 |
| Number of pages | 14 |
| Journal | Condensed Matter Physics |
| Volume | 10 |
| Issue number | 4 |
| Publication status | Published - 2007 |
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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 journal › Article
}
TY - JOUR
T1 - Combination of generalized-ensemble algorithms and one-dimensional reference interaction site model theory
AU - Mitsutake, A.
AU - Kinoshita, M.
AU - Hirata, F.
AU - Okamoto, Y.
PY - 2007
Y1 - 2007
N2 - 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.
AB - 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.
KW - Generalized-ensemble algorithm
KW - Monte Carlo
KW - Multicanonical algorithm
KW - Protein folding
KW - Replica-exchange method
KW - RISM
UR - http://www.scopus.com/inward/record.url?scp=38149009036&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=38149009036&partnerID=8YFLogxK
M3 - Article
AN - SCOPUS:38149009036
VL - 10
SP - 495
EP - 508
JO - Condensed Matter Physics
JF - Condensed Matter Physics
SN - 1607-324X
IS - 4
ER -