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Anders Irbäck and Sandipan Mohanty
PROFASI: a Monte Carlo simulation package for
protein folding and aggregation
Journal of Computational Chemistry 27,
1548-1555 (2006)
Abstract
We present a flexible and efficient program package
written in C++, PROFASI, for simulating protein folding
and aggregation. The systems are modeled using an
all-atom description of the protein chains with only
torsional degrees of freedom, and implicit water. The
program package has a modular structure that makes the
interaction potential easy to modify. The currently
implemented potential is able to fold several peptides
with about 20 residues, and has also been used to study
aggregation and force-induced unfolding. The simulation
methods implemented in PROFASI are Monte Carlo-based and
include a semi-local move and simulated tempering. Adding
new updates is easy. The code runs fast in both single-
and multi-chain applications, as is illustrated by
several examples.
LU TP 05-38
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