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Items: 1 to 20 of 113

1.

MSMBuilder: Statistical Models for Biomolecular Dynamics.

Harrigan MP, Sultan MM, Hernández CX, Husic BE, Eastman P, Schwantes CR, Beauchamp KA, McGibbon RT, Pande VS.

Biophys J. 2017 Jan 10;112(1):10-15. doi: 10.1016/j.bpj.2016.10.042.

2.

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.

3.

A tutorial on building markov state models with MSMBuilder and coarse-graining them with BACE.

Bowman GR.

Methods Mol Biol. 2014;1084:141-58. doi: 10.1007/978-1-62703-658-0_8.

PMID:
24061920
4.

Progress and challenges in the automated construction of Markov state models for full protein systems.

Bowman GR, Beauchamp KA, Boxer G, Pande VS.

J Chem Phys. 2009 Sep 28;131(12):124101. doi: 10.1063/1.3216567.

5.

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.

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.

Transition path theory analysis of c-Src kinase activation.

Meng Y, Shukla D, Pande VS, Roux B.

Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):9193-8. doi: 10.1073/pnas.1602790113. Epub 2016 Aug 1.

8.

Application of Markov State Models to simulate long timescale dynamics of biological macromolecules.

Da LT, Sheong FK, Silva DA, Huang X.

Adv Exp Med Biol. 2014;805:29-66. doi: 10.1007/978-3-319-02970-2_2.

PMID:
24446356
9.

Application of Hidden Markov Models in Biomolecular Simulations.

Shukla S, Shamsi Z, Moffett AS, Selvam B, Shukla D.

Methods Mol Biol. 2017;1552:29-41. doi: 10.1007/978-1-4939-6753-7_3.

PMID:
28224489
10.

Markov State Models: From an Art to a Science.

Husic BE, Pande VS.

J Am Chem Soc. 2018 Feb 21;140(7):2386-2396. doi: 10.1021/jacs.7b12191. Epub 2018 Feb 2. Review.

PMID:
29323881
11.

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.

12.

Markov models for the elucidation of allosteric regulation.

Sengupta U, Strodel B.

Philos Trans R Soc Lond B Biol Sci. 2018 Jun 19;373(1749). pii: 20170178. doi: 10.1098/rstb.2017.0178. Review.

PMID:
29735732
13.

Statistical model selection for Markov models of biomolecular dynamics.

McGibbon RT, Schwantes CR, Pande VS.

J Phys Chem B. 2014 Jun 19;118(24):6475-81. doi: 10.1021/jp411822r. Epub 2014 Apr 25.

PMID:
24738580
14.

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.

Parton DL, Grinaway PB, Hanson SM, Beauchamp KA, Chodera JD.

PLoS Comput Biol. 2016 Jun 23;12(6):e1004728. doi: 10.1371/journal.pcbi.1004728. eCollection 2016 Jun.

15.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
16.

Building Markov State Models for Periodically Driven Non-Equilibrium Systems.

Wang H, Schütte C.

J Chem Theory Comput. 2015 Apr 14;11(4):1819-31.

PMID:
26889513
17.

Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning.

Matsunaga Y, Sugita Y.

Elife. 2018 May 3;7. pii: e32668. doi: 10.7554/eLife.32668.

18.

Heat dissipation guides activation in signaling proteins.

Weber JK, Shukla D, Pande VS.

Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10377-82. doi: 10.1073/pnas.1501804112. Epub 2015 Aug 3.

19.

Sarment: Python modules for HMM analysis and partitioning of sequences.

Guéguen L.

Bioinformatics. 2005 Aug 15;21(16):3427-8. Epub 2005 Jun 9.

PMID:
15947017
20.

MSMExplorer: visualizing Markov state models for biomolecule folding simulations.

Cronkite-Ratcliff B, Pande V.

Bioinformatics. 2013 Apr 1;29(7):950-2. doi: 10.1093/bioinformatics/btt051. Epub 2013 Jan 30.

PMID:
23365411

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