Testing a new Monte Carlo Algorithm for Protein Folding

Details Testing a new Monte Carlo Algorithm for Protein Folding Testing a new Monte Carlo Algorithm for Protein Folding

1997-10-02

arxiv.org/abs/cond-mat/9710030v1

Proteins: Structure, Function, and Genetics Vol. 32 (1998) 52--66

Physics

Condensed Matter

Statistical Mechanics

13 pages, RevTeX, needs epsfig.sty and multicolum.sty

Scientific paper

We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P. Grassberger, Phys. Rev. E, in press (1997)) leads to extremely 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.

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