Protein Folding Simulations by Generalized-Ensemble Algorithms
Yuko Okamoto
Department of Theoretical Studies
Institute for Molecular Science
Okazaki, Aichi 444-8585
JAPAN
Abstract
The difficulty in molecular simulations of complex systems
comes from the fact that there exist an astronomically large
number of local minima in the energy function, forcing
conventional constant-temperature canonical simulations to
get trapped in a few states of the energy local minima.
Novel algorithms that can alleviate this multiple-minima
problem are thus in urgent demand. We have been advocating
the uses of the generalized-ensemble algorithms.
Generalized-ensemble algorithms, which are based on
artificial non-Boltzmann weight factors, alleviate this
multiple-minima problem by performing random walks in potential
energy space. The advantage of these algorithms lies in the
fact that from only one simulation run, one can obtain not only
the global-minimum state in potential energy but also various
thermodynamic quantities as a function of temperature. They are
thus particularly useful for free energy calculations.
Multicanonical algorithm, simulated tempering, and
replica-exchange method (also referred to as parallel-tempering)
are well-known examples of generalized-ensemble algorithms and
have been widely used in protein folding simulations.
In this talk, I will present some of the latest results of our
generalized-ensemble simulations in protein folding.