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Testing a new Monte Carlo algorithm for protein folding
Author(s) -
Bastolla Ugo,
Frauenkron Helge,
Gerstner Erwin,
Grassberger Peter,
Nadler Walter
Publication year - 1998
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19980701)32:1<52::aid-prot7>3.0.co;2-g
Subject(s) - monte carlo method , statistical physics , algorithm , folding (dsp implementation) , computer science , lattice (music) , simple (philosophy) , protein folding , biological system , physics , mathematics , engineering , statistics , biology , philosophy , epistemology , nuclear magnetic resonance , acoustics , electrical engineering
We demonstrate that the recently proposed pruned‐enriched Rosenbluth method (PERM) (Grassberger, Phys. Rev. E 56:3682, 1997) leads to extremely efficient algorithms for the folding of simple model proteins. We test it on several models for lattice heteropolymers, and compare it 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 one to analyze thermodynamic aspects of the folding behavior of arbitrary sequences. Proteins 32:52–66, 1998. © 1998 Wiley‐Liss, Inc.