1998/06/26 by H. Frauenkron, Helge Frauenkron, Ugo Bastolla +11
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #FOS: Biological sciences #FOS: Physical sciences #Protein Structure and Dynamics #Quantitative Biology (q-bio) #Soft Condensed Matter (cond-mat.soft) #cond-mat.soft #q-bio
paper · pdf · doi:10.48550/arxiv.cond-mat/9806323
17 pages, 21 figures, needs mprocl.sty (included), appears in Workshop on: Monte Carlo Approach to Biopolymers and Protein Folding, World Scientific 1998
arxiv created 1998/06/26 · openalex publication_date 1998/06/26 · arxiv updated 2009/11/30 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.