Testing a New Monte Carlo Strategy for Folding Model Proteins
Abstract
We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P.~Grassberger, Phys.~Rev.~{\bf E 56} (1997) 3682) leads to very efficient algorithms for the folding of simple model proteins. We test it on several models for lattice heteropolymers, and compare to published Monte Carlo studies of the properties of particular sequences. In all cases our method is faster than the previous ones, and in several cases we find new minimal energy states. In addition to producing more reliable candidates for ground states, our method gives detailed information about the thermal spectrum and, thus, allows to analyze static aspects of the folding behavior of arbitrary sequences.
Cite
@article{arxiv.cond-mat/9806323,
title = {Testing a New Monte Carlo Strategy for Folding Model Proteins},
author = {H. Frauenkron and U. Bastolla and E. Gerstner and P. Grassberger and und W. Nadler},
journal= {arXiv preprint arXiv:cond-mat/9806323},
year = {2007}
}
Comments
17 pages, 21 figures, needs mprocl.sty (included), appears in Workshop on: Monte Carlo Approach to Biopolymers and Protein Folding, World Scientific 1998