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Comparison of predicted native structures of Met-enkephalin based on various accessible-surface-area solvent models

✍ Scribed by Lixin Zhan; Jeff Z. Y. Chen; Wing-Ki Liu

Publisher
John Wiley and Sons
Year
2009
Tongue
English
Weight
183 KB
Volume
30
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

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

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