Generalized-Ensemble Algorithms for Protein Folding and Unfolding

Author(s): Yuko Okamoto.

Journal Name: Current Physical Chemistry

Volume 2 , Issue 1 , 2012

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Abstract:

When one studies protein folding and unfolding by molecular simulations, one faces a great difficulty. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in local-minimum-energy states, giving the results in error. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. In this article we review some of powerful generalized-ensemble algorithms, namely, replica-exchange method, simulated tempering, and multicanonical algorithm, and their multidimensional/multivariable extensions.

Keywords: Canonical ensemble, Generalized-ensemble algorithm, Isobaric-isothermal ensemble, Molecular dynamics (MD), Molecular simulation, Monte Carlo (MC), Multicanonical algorithm (MUCA), Multicanonical replica-exchange method (MUCAREM), Multidimensional generalized-ensemble algorithm, , Pressure-induced denaturation, Protein folding, Protein unfolding, Replica-exchange method (REM), Replica-exchange molecular dynamics (REMD), Simulated tempering (ST)

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Article Details

VOLUME: 2
ISSUE: 1
Year: 2012
Page: [92 - 106]
Pages: 15
DOI: 10.2174/1877946811202010092

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