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Items: 1 to 20 of 102

1.

Adaptive Markov state model estimation using short reseeding trajectories.

Wan H, Voelz VA.

J Chem Phys. 2020 Jan 14;152(2):024103. doi: 10.1063/1.5142457.

PMID:
31941308
2.

Markov state model reveals folding and functional dynamics in ultra-long MD trajectories.

Lane TJ, Bowman GR, Beauchamp K, Voelz VA, Pande VS.

J Am Chem Soc. 2011 Nov 16;133(45):18413-9. doi: 10.1021/ja207470h. Epub 2011 Oct 26.

3.

Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics.

Sinitskiy AV, Pande VS.

J Chem Phys. 2018 Jan 28;148(4):044111. doi: 10.1063/1.5005058.

4.

How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory.

Deng NJ, Dai W, Levy RM.

J Phys Chem B. 2013 Oct 24;117(42):12787-99. doi: 10.1021/jp401962k. Epub 2013 Jun 13.

5.

Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models.

Suárez E, Adelman JL, Zuckerman DM.

J Chem Theory Comput. 2016 Aug 9;12(8):3473-81. doi: 10.1021/acs.jctc.6b00339. Epub 2016 Jul 11.

6.

Markov state models provide insights into dynamic modulation of protein function.

Shukla D, Hernández CX, Weber JK, Pande VS.

Acc Chem Res. 2015 Feb 17;48(2):414-22. doi: 10.1021/ar5002999. Epub 2015 Jan 3. Review.

7.

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
8.

A new class of enhanced kinetic sampling methods for building Markov state models.

Bhoutekar A, Ghosh S, Bhattacharya S, Chatterjee A.

J Chem Phys. 2017 Oct 21;147(15):152702. doi: 10.1063/1.4984932.

9.

High-Resolution Markov State Models for the Dynamics of Trp-Cage Miniprotein Constructed Over Slow Folding Modes Identified by State-Free Reversible VAMPnets.

Sidky H, Chen W, Ferguson AL.

J Phys Chem B. 2019 Sep 26;123(38):7999-8009. doi: 10.1021/acs.jpcb.9b05578. Epub 2019 Sep 16.

PMID:
31453697
10.

Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes.

Zimmerman MI, Porter JR, Sun X, Silva RR, Bowman GR.

J Chem Theory Comput. 2018 Nov 13;14(11):5459-5475. doi: 10.1021/acs.jctc.8b00500. Epub 2018 Oct 23.

11.
12.

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39).

Voelz VA, Bowman GR, Beauchamp K, Pande VS.

J Am Chem Soc. 2010 Feb 10;132(5):1526-8. doi: 10.1021/ja9090353.

13.

Set-free Markov state model building.

Weber M, Fackeldey K, Schütte C.

J Chem Phys. 2017 Mar 28;146(12):124133. doi: 10.1063/1.4978501.

PMID:
28388134
14.
15.

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.

16.

Metadynamics Enhanced Markov Modeling of Protein Dynamics.

Biswas M, Lickert B, Stock G.

J Phys Chem B. 2018 May 31;122(21):5508-5514. doi: 10.1021/acs.jpcb.7b11800. Epub 2018 Jan 27.

PMID:
29338243
17.

From molecular energy landscapes to equilibrium dynamics via landscape analysis and markov state models.

Kabir KL, Akhter N, Shehu A.

J Bioinform Comput Biol. 2019 Dec;17(6):1940014. doi: 10.1142/S0219720019400146.

PMID:
32019409
18.

Computing long time scale biomolecular dynamics using quasi-stationary distribution kinetic Monte Carlo (QSD-KMC).

Agarwal A, Hengartner NW, Gnanakaran S, Voter AF.

J Chem Phys. 2019 Aug 21;151(7):074109. doi: 10.1063/1.5094457.

PMID:
31438708
19.

Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics.

McGibbon RT, Pande VS.

J Chem Theory Comput. 2013 Jul 9;9(7):2900-6. doi: 10.1021/ct400132h. Epub 2013 Jun 6.

PMID:
26583974
20.

An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling.

Wang W, Liang T, Sheong FK, Fan X, Huang X.

J Chem Phys. 2018 Aug 21;149(7):072337. doi: 10.1063/1.5027001.

PMID:
30134698

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