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Items: 1 to 20 of 94

1.

Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State Models.

Voelz VA, Elman B, Razavi AM, Zhou G.

J Chem Theory Comput. 2014 Dec 9;10(12):5716-28. doi: 10.1021/ct500827g.

PMID:
26583253
2.

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.

3.
4.

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
5.

A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations.

Wan H, Zhou G, Voelz VA.

J Chem Theory Comput. 2016 Dec 13;12(12):5768-5776. Epub 2016 Nov 23.

PMID:
27951664
6.

Using generalized ensemble simulations and Markov state models to identify conformational states.

Bowman GR, Huang X, Pande VS.

Methods. 2009 Oct;49(2):197-201. doi: 10.1016/j.ymeth.2009.04.013. Epub 2009 May 4.

7.
8.

Automatic state partitioning for multibody systems (APM): an efficient algorithm for constructing Markov state models to elucidate conformational dynamics of multibody systems.

Sheong FK, Silva DA, Meng L, Zhao Y, Huang X.

J Chem Theory Comput. 2015 Jan 13;11(1):17-27. doi: 10.1021/ct5007168. Epub 2014 Dec 23.

PMID:
26574199
9.

Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules.

Noé F, Wu H, Prinz JH, Plattner N.

J Chem Phys. 2013 Nov 14;139(18):184114. doi: 10.1063/1.4828816.

PMID:
24320261
10.

Enhanced modeling via network theory: Adaptive sampling of Markov state models.

Bowman GR, Ensign DL, Pande VS.

J Chem Theory Comput. 2010;6(3):787-94.

11.

Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

Noé F, Horenko I, Schütte C, Smith JC.

J Chem Phys. 2007 Apr 21;126(15):155102.

PMID:
17461666
12.

Markov state models based on milestoning.

Schütte C, Noé F, Lu J, Sarich M, Vanden-Eijnden E.

J Chem Phys. 2011 May 28;134(20):204105. doi: 10.1063/1.3590108.

PMID:
21639422
13.

Simulating the T-jump-triggered unfolding dynamics of trpzip2 peptide and its time-resolved IR and two-dimensional IR signals using the Markov state model approach.

Zhuang W, Cui RZ, Silva DA, Huang X.

J Phys Chem B. 2011 May 12;115(18):5415-24. doi: 10.1021/jp109592b. Epub 2011 Mar 9.

PMID:
21388153
14.

Conformational transition in signal transduction: metastable states and transition pathways in the activation of a signaling protein.

Banerjee R, Yan H, Cukier RI.

J Phys Chem B. 2015 Jun 4;119(22):6591-602. doi: 10.1021/acs.jpcb.5b02582. Epub 2015 May 19.

PMID:
25945797
15.

Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms.

Huang X, Yao Y, Bowman GR, Sun J, Guibas LJ, Carlsson G, Pande VS.

Pac Symp Biocomput. 2010:228-39.

16.

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
17.

Transition networks for modeling the kinetics of conformational change in macromolecules.

Noé F, Fischer S.

Curr Opin Struct Biol. 2008 Apr;18(2):154-62. doi: 10.1016/j.sbi.2008.01.008. Review.

PMID:
18378442
18.

Mechanism for the alpha-helix to beta-hairpin transition.

Ding F, Borreguero JM, Buldyrey SV, Stanley HE, Dokholyan NV.

Proteins. 2003 Nov 1;53(2):220-8.

PMID:
14517973
19.

Structural and thermodynamics characters of isolated α-syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution.

Cao Z, Liu L, Wu P, Wang J.

Acta Biochim Biophys Sin (Shanghai). 2011 Mar;43(3):172-80. doi: 10.1093/abbs/gmr002. Epub 2011 Feb 2. Erratum in: Acta Biochim Biophys Sin (Shanghai). 2011 Apr;43(4):335.

PMID:
21289072
20.

EMMA: A Software Package for Markov Model Building and Analysis.

Senne M, Trendelkamp-Schroer B, Mey AS, Schütte C, Noé F.

J Chem Theory Comput. 2012 Jul 10;8(7):2223-38. doi: 10.1021/ct300274u. Epub 2012 Jun 18.

PMID:
26588955

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