Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 136

1.

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.

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.

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
4.

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.

5.
6.

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.

7.

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.

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.

Markov dynamic models for long-timescale protein motion.

Chiang TH, Hsu D, Latombe JC.

Bioinformatics. 2010 Jun 15;26(12):i269-77. doi: 10.1093/bioinformatics/btq177.

10.

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
11.

Protein folded states are kinetic hubs.

Bowman GR, Pande VS.

Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10890-5. doi: 10.1073/pnas.1003962107. Epub 2010 Jun 1. Erratum in: Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16749.

12.

Simulating the peptide folding kinetic related spectra based on the Markov State Model.

Song J, Zhuang W.

Adv Exp Med Biol. 2014;805:199-220. doi: 10.1007/978-3-319-02970-2_9. Review.

PMID:
24446363
13.

Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables.

Prinz JH, Keller B, Noé F.

Phys Chem Chem Phys. 2011 Oct 14;13(38):16912-27. doi: 10.1039/c1cp21258c. Epub 2011 Aug 22.

PMID:
21858310
14.

Markov models of molecular kinetics: generation and validation.

Prinz JH, Wu H, Sarich M, Keller B, Senne M, Held M, Chodera JD, Schütte C, Noé F.

J Chem Phys. 2011 May 7;134(17):174105. doi: 10.1063/1.3565032.

PMID:
21548671
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.

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.

17.

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
18.

Modeling protein thermodynamics and fluctuations at the mesoscale.

Nakagawa N, Peyrard M.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Oct;74(4 Pt 1):041916. Epub 2006 Oct 25.

PMID:
17155105
19.

Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments.

Beauchamp KA, Ensign DL, Das R, Pande VS.

Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12734-9. doi: 10.1073/pnas.1010880108. Epub 2011 Jul 18.

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

Supplemental Content

Support Center