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Mixed monte carlo/molecular dynamics simulations in explicit solvent

✍ Scribed by André A. S. T. Ribeiro; Ricardo B. de Alencastro

Publisher
John Wiley and Sons
Year
2012
Tongue
English
Weight
953 KB
Volume
33
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

A mixed Monte Carlo/Molecular Dynamics method using the trial moves for peptide backbone sampling known as Concerted Rotations with Angles was implemented. The algorithm was used to study polyalanine systems. Equivalent results to conventional Molecular Dynamics were obtained for simulations of Ala~6~ in implicit solvent. To test the efficiency of the implemented method, several 150 ns simulations of Ala~12~ in explicit water were performed. The results show that the present method yields significantly faster formation of secondary structure than the conventional Molecular Dynamics simulations. This opens the possibility to selectively sample alanine‐rich regions of larger peptides or proteins. It remains to be established whether hydrophilic amino acid residues can be successfully treated with the present methodology. © 2012 Wiley Periodicals, Inc.

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