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231223s2011 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.21626
|2 doi
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|a eng
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|a Mamonov, Artem B
|e verfasserin
|4 aut
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|a Rapid sampling of all-atom peptides using a library-based polymer-growth approach
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|c 2011
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
|b c
|2 rdamedia
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|a ƒa Online-Ressource
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|2 rdacarrier
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|a Date Completed 05.04.2011
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|a Date Revised 23.03.2024
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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|a Copyright © 2010 Wiley Periodicals, Inc.
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|a We adapted existing polymer growth strategies for equilibrium sampling of peptides described by modern atomistic forcefields with a simple uniform dielectric solvent. The main novel feature of our approach is the use of precalculated statistical libraries of molecular fragments. A molecule is sampled by combining fragment configurations-of single residues in this study-which are stored in the libraries. Ensembles generated from the independent libraries are reweighted to conform with the Boltzmann-factor distribution of the forcefield describing the full molecule. In this way, high-quality equilibrium sampling of small peptides (4-8 residues) typically requires less than one hour of single-processor wallclock time and can be significantly faster than Langevin simulations. Furthermore, approximate, clash-free ensembles can be generated for larger peptides (up to 32 residues in this study) in less than a minute of single-processor computing. We discuss possible applications of our growth procedure to free energy calculation, fragment assembly protein-structure prediction protocols, and to "multi-resolution" sampling
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|a Journal Article
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|a Research Support, N.I.H., Extramural
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|a Research Support, U.S. Gov't, Non-P.H.S.
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|a Peptides
|2 NLM
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|a Polymers
|2 NLM
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|a Zhang, Xin
|e verfasserin
|4 aut
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|a Zuckerman, Daniel M
|e verfasserin
|4 aut
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 32(2011), 3 vom: 07. Feb., Seite 396-405
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|x 1096-987X
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|g volume:32
|g year:2011
|g number:3
|g day:07
|g month:02
|g pages:396-405
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|u http://dx.doi.org/10.1002/jcc.21626
|3 Volltext
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