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Items: 1 to 20 of 158

1.

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.

Prinz JH, Chodera JD, Pande VS, Swope WC, Smith JC, Noé F.

J Chem Phys. 2011 Jun 28;134(24):244108. doi: 10.1063/1.3592153.

2.

Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.

Chodera JD, Swope WC, Noé F, Prinz JH, Shirts MR, Pande VS.

J Chem Phys. 2011 Jun 28;134(24):244107. doi: 10.1063/1.3592152.

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5.

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states.

Wu H, Mey AS, Rosta E, Noé F.

J Chem Phys. 2014 Dec 7;141(21):214106. doi: 10.1063/1.4902240.

PMID:
25481128
6.

Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides.

Narayan B, Herbert C, Yuan Y, Rodriguez BJ, Brooks BR, Buchete NV.

J Chem Phys. 2018 Aug 21;149(7):072323. doi: 10.1063/1.5027580.

PMID:
30134732
7.

A Bayesian method for construction of Markov models to describe dynamics on various time-scales.

Rains EK, Andersen HC.

J Chem Phys. 2010 Oct 14;133(14):144113. doi: 10.1063/1.3496438.

PMID:
20949993
8.
9.

Gaussian Markov transition models of molecular kinetics.

Wu H, Noé F.

J Chem Phys. 2015 Feb 28;142(8):084104. doi: 10.1063/1.4913214.

PMID:
25725709
10.

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint.

Bacallado S, Chodera JD, Pande V.

J Chem Phys. 2009 Jul 28;131(4):045106. doi: 10.1063/1.3192309.

11.

Identifying and correcting non-Markov states in peptide conformational dynamics.

Nerukh D, Jensen CH, Glen RC.

J Chem Phys. 2010 Feb 28;132(8):084104. doi: 10.1063/1.3328781.

PMID:
20192287
12.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions.

Nedialkova LV, Amat MA, Kevrekidis IG, Hummer G.

J Chem Phys. 2014 Sep 21;141(11):114102. doi: 10.1063/1.4893963.

13.

Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution.

Trendelkamp-Schroer B, Noé F.

J Chem Phys. 2013 Apr 28;138(16):164113. doi: 10.1063/1.4801325.

PMID:
23635117
14.

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

Zheng W, Gallicchio E, Deng N, Andrec M, Levy RM.

J Phys Chem B. 2011 Feb 17;115(6):1512-23. doi: 10.1021/jp1089596. Epub 2011 Jan 21.

15.

Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study.

de Oliveira CA, Hamelberg D, McCammon JA.

J Chem Phys. 2007 Nov 7;127(17):175105.

PMID:
17994855
16.

Hierarchical Nyström methods for constructing Markov state models for conformational dynamics.

Yao Y, Cui RZ, Bowman GR, Silva DA, Sun J, Huang X.

J Chem Phys. 2013 May 7;138(17):174106. doi: 10.1063/1.4802007.

PMID:
23656113
17.

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.

Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC.

J Chem Phys. 2007 Apr 21;126(15):155101.

PMID:
17461665
18.

Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.

Yi Z, Lindner B, Prinz JH, Noé F, Smith JC.

J Chem Phys. 2013 Nov 7;139(17):175102. doi: 10.1063/1.4824071.

PMID:
24206335
19.

Identification of slow molecular order parameters for Markov model construction.

Pérez-Hernández G, Paul F, Giorgino T, De Fabritiis G, Noé F.

J Chem Phys. 2013 Jul 7;139(1):015102. doi: 10.1063/1.4811489.

PMID:
23822324
20.

Markov state models of biomolecular conformational dynamics.

Chodera JD, Noé F.

Curr Opin Struct Biol. 2014 Apr;25:135-44. doi: 10.1016/j.sbi.2014.04.002. Epub 2014 May 16. Review.

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