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Monte carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space
Author(s) -
Caflisch Amedeo,
Niederer Peter,
Anliker Max
Publication year - 1992
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/prot.340140111
Subject(s) - maxima and minima , thermalisation , cartesian coordinate system , monte carlo method , pentapeptide repeat , minification , global optimization , energy minimization , space (punctuation) , statistical physics , physics , chemistry , mathematics , computational chemistry , thermodynamics , computer science , mathematical analysis , mathematical optimization , geometry , peptide , nuclear magnetic resonance , statistics , operating system
A new minimization procedure for the global optimization is cartesian coordinate space of the conformational energy of a polypeptide chain is presented. The Metropolis Monte Carlo minimization is thereby supplemented by a thermalization process, which is initiated whenever a structure becomes trapped in an area containing closely located local minima in the conformational space. The method has been applied to the endogenous opioid pentapeptide methionine enkephalin. Five among 13 different starting conformations led to the same apparent global minimum of an in‐house developed energy function, a type II′ reverse turn, the central residues of which are Gly‐3‐Phe‐4. A comparison between the ECEPP/2 global minimum conformation of methionine enkephalin and the apparent one achieved by the present method shows that minimum‐energy conformations having a certain similarity can be generated by relatively different force fields. © 1992 Wiley‐Liss, Inc.