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Items: 1 to 20 of 105

1.

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
2.

Molecular Dynamics-Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit.

Thayer KM, Lakhani B, Beveridge DL.

J Phys Chem B. 2017 Jun 8;121(22):5509-5514. doi: 10.1021/acs.jpcb.7b02083. Epub 2017 May 25.

PMID:
28489401
3.

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
4.

Optimized parameter selection reveals trends in Markov state models for protein folding.

Husic BE, McGibbon RT, Sultan MM, Pande VS.

J Chem Phys. 2016 Nov 21;145(19):194103.

5.

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
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.

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.

8.

A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models.

Husic BE, McKiernan KA, Wayment-Steele HK, Sultan MM, Pande VS.

J Chem Theory Comput. 2018 Feb 13;14(2):1071-1082. doi: 10.1021/acs.jctc.7b01004. Epub 2018 Jan 24.

PMID:
29253336
9.

Ward Clustering Improves Cross-Validated Markov State Models of Protein Folding.

Husic BE, Pande VS.

J Chem Theory Comput. 2017 Mar 14;13(3):963-967. doi: 10.1021/acs.jctc.6b01238. Epub 2017 Feb 17.

PMID:
28195713
10.

Why are MD simulated protein folding times wrong?

Nerukhdn D.

Adv Exp Med Biol. 2010;680:321-6. doi: 10.1007/978-1-4419-5913-3_36.

PMID:
20865515
11.

Markov state models of protein misfolding.

Sirur A, De Sancho D, Best RB.

J Chem Phys. 2016 Feb 21;144(7):075101. doi: 10.1063/1.4941579.

12.

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
13.

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.

14.
15.

Using Markov state models to study self-assembly.

Perkett MR, Hagan MF.

J Chem Phys. 2014 Jun 7;140(21):214101. doi: 10.1063/1.4878494.

16.

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
17.

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
18.

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.

19.

Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models.

Dixit PD, Dill KA.

J Chem Theory Comput. 2018 Feb 13;14(2):1111-1119. doi: 10.1021/acs.jctc.7b01126. Epub 2018 Jan 26.

PMID:
29323898
20.

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.

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