| A New Multiscale Algorithm and its Application to Coarse-Grained Peptide Models for Self-Assembly. | |
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MedLine Citation:
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PMID: 22300263 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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Peptide self-assembly plays a role in a number of diseases, in pharmaceutical degradation, and in emerging biomaterials. Here we aim to develop an accurate molecular-scale picture of this process using a multiscale computational approach. Recently, Shell [Shell, M. S., J. Chem. Phys. 2008, 129, 144108] developed a coarse-graining methodology that is based on a thermodynamic quantity called the relative entropy, a measure of how different two molecular ensembles behave. By minimizing the relative entropy between a coarse-grained peptide system and a reference all-atom system, with respect to the coarse-grained model's force-field parameters, an optimized coarse-grained model can be obtained. We have reformulated this methodology using a trajectory-reweighting and perturbation strategy that enables complex coarse-grained models with at least 100s of parameters to be optimized efficiently. This new algorithm allows for complex peptide systems to be coarse-grained into much simpler models that nonetheless recapitulate many correct features of detailed all-atom ones. In particular, we present results for a polyalanine case study, with attention to both individual peptide folding and large-scale fibril assembly. |
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Authors:
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Scott Patrick Carmichael; M Scott Shell |
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Publication Detail:
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Type: JOURNAL ARTICLE Date: 2012-2-2 |
Journal Detail:
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Title: The journal of physical chemistry. B Volume: - ISSN: 1520-5207 ISO Abbreviation: - Publication Date: 2012 Feb |
Date Detail:
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Created Date: 2012-2-3 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 101157530 Medline TA: J Phys Chem B Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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