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Comparison of predicted native structures of Met‐enkephalin based on various accessible‐surface‐area solvent models
Author(s) -
Zhan Lixin,
Chen Jeff Z. Y.,
Liu WingKi
Publication year - 2009
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21129
Subject(s) - solvent , similarity (geometry) , monte carlo method , surface (topology) , accessible surface area , surface protein , computational science and engineering , statistical physics , chemistry , computer science , mathematics , computational chemistry , physics , geometry , statistics , artificial intelligence , biology , organic chemistry , image (mathematics) , virology
We examine the variation and similarity of the native structures predicted from various accessible‐surface‐area solvent models for peptide Met‐enkephalin. Both ECEPP/2 and ECEPP/3 force fields have been used in conjunction with ten different sets of accessible‐surface‐area parameterization. The native structures were determined by an implementation of the basin hopping Monte Carlo technique. The results suggest that the implicit solvent models examined in this study should be employed in computer simulations with extreme caution. In addition, the effect of fixing or not fixing the peptide angles ω has been examined. We conclude that fixing ω generally gives rise to a poor prediction. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009