Generalized-Ensemble Algorithms for Protein Folding and Unfolding

Yuko      Okamoto

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)