| Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty. | |
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MedLine Citation:
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PMID: 23039589 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Markov state models (MSMs)--or discrete-time master equation models--are a powerful way of modeling the structure and function of molecular systems like proteins. Unfortunately, MSMs with sufficiently many states to make a quantitative connection with experiments (often tens of thousands of states even for small systems) are generally too complicated to understand. Here, I present a bayesian agglomerative clustering engine (BACE) for coarse-graining such Markov models, thereby reducing their complexity and making them more comprehensible. An important feature of this algorithm is its ability to explicitly account for statistical uncertainty in model parameters that arises from finite sampling. This advance builds on a number of recent works highlighting the importance of accounting for uncertainty in the analysis of MSMs and provides significant advantages over existing methods for coarse-graining Markov state models. The closed-form expression I derive here for determining which states to merge is equivalent to the generalized Jensen-Shannon divergence, an important measure from information theory that is related to the relative entropy. Therefore, the method has an appealing information theoretic interpretation in terms of minimizing information loss. The bottom-up nature of the algorithm likely makes it particularly well suited for constructing mesoscale models. I also present an extremely efficient expression for bayesian model comparison that can be used to identify the most meaningful levels of the hierarchy of models from BACE. |
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Authors:
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Gregory R Bowman |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: The Journal of chemical physics Volume: 137 ISSN: 1089-7690 ISO Abbreviation: J Chem Phys Publication Date: 2012 Oct |
Date Detail:
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Created Date: 2012-10-08 Completed Date: 2013-02-20 Revised Date: 2013-04-16 |
Medline Journal Info:
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Nlm Unique ID: 0375360 Medline TA: J Chem Phys Country: United States |
Other Details:
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Languages: eng Pagination: 134111 Citation Subset: IM |
Affiliation:
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Department of Chemistry, University of California, Berkeley, California 94720, USA. gregoryrbowman@gmail.com |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms Kinetics Markov Chains* Proteins / chemistry* Thermodynamics Uncertainty |
| Grant Support | |
ID/Acronym/Agency:
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R01-GM050945/GM/NIGMS NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/Proteins |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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