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The social network (of protein conformations).

作者信息

Chodera John D, Pande Vijay S

机构信息

California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.

出版信息

Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):12969-70. doi: 10.1073/pnas.1109571108. Epub 2011 Jul 29.

Abstract
摘要

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本文引用的文献

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From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map.
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Markov models of molecular kinetics: generation and validation.
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Determination of reaction coordinates via locally scaled diffusion map.
J Chem Phys. 2011 Mar 28;134(12):124116. doi: 10.1063/1.3569857.
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Everything you wanted to know about Markov State Models but were afraid to ask.
Methods. 2010 Sep;52(1):99-105. doi: 10.1016/j.ymeth.2010.06.002. Epub 2010 Jun 4.
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Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.
Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19011-6. doi: 10.1073/pnas.0905466106. Epub 2009 Nov 3.
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Reactive flux and folding pathways in network models of coarse-grained protein dynamics.
J Chem Phys. 2009 May 28;130(20):205102. doi: 10.1063/1.3139063.
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Full correlation analysis of conformational protein dynamics.
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Calculation of the free energy and cooperativity of protein folding.
PLoS One. 2007 May 16;2(5):e446. doi: 10.1371/journal.pone.0000446.
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Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction.
Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9885-90. doi: 10.1073/pnas.0603553103. Epub 2006 Jun 19.
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