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Results: 1 to 20 of 122

1.

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
[PubMed - indexed for MEDLINE]
2.

A role for both conformational selection and induced fit in ligand binding by the LAO protein.

Silva DA, Bowman GR, Sosa-Peinado A, Huang X.

PLoS Comput Biol. 2011 May;7(5):e1002054. doi: 10.1371/journal.pcbi.1002054. Epub 2011 May 26.

PMID:
21637799
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
19908375
[PubMed - indexed for MEDLINE]
Free Article
4.

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
[PubMed - as supplied by publisher]
5.

Efficient traversal of beta-sheet protein folding pathways using ensemble models.

Shenker S, O'Donnell CW, Devadas S, Berger B, Waldispühl J.

J Comput Biol. 2011 Nov;18(11):1635-47. doi: 10.1089/cmb.2011.0176. Epub 2011 Sep 29.

PMID:
21958108
[PubMed - indexed for MEDLINE]
6.

Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis.

Naritomi Y, Fuchigami S.

J Chem Phys. 2013 Dec 7;139(21):215102. doi: 10.1063/1.4834695.

PMID:
24320404
[PubMed - indexed for MEDLINE]
7.

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.

Ditzler MA, Otyepka M, Sponer J, Walter NG.

Acc Chem Res. 2010 Jan 19;43(1):40-7. doi: 10.1021/ar900093g.

PMID:
19754142
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
21988563
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
19791846
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
24836551
[PubMed - in process]
11.

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
[PubMed - indexed for MEDLINE]
12.

Frontiers in molecular dynamics simulations of DNA.

Pérez A, Luque FJ, Orozco M.

Acc Chem Res. 2012 Feb 21;45(2):196-205. doi: 10.1021/ar2001217. Epub 2011 Aug 10. Review.

PMID:
21830782
[PubMed - indexed for MEDLINE]
13.

Nuclear magnetic resonance signal chemical shifts and molecular simulations: a multidisciplinary approach to modeling copper protein structures.

Sgrignani J, Pierattelli R.

J Biol Inorg Chem. 2012 Jan;17(1):71-9. doi: 10.1007/s00775-011-0830-7. Epub 2011 Aug 13.

PMID:
21842229
[PubMed - indexed for MEDLINE]
14.

Atomic-level characterization of the structural dynamics of proteins.

Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W.

Science. 2010 Oct 15;330(6002):341-6. doi: 10.1126/science.1187409.

PMID:
20947758
[PubMed - indexed for MEDLINE]
Free Article
15.

A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase.

Da LT, Pardo Avila F, Wang D, Huang X.

PLoS Comput Biol. 2013 Apr;9(4):e1003020. doi: 10.1371/journal.pcbi.1003020. Epub 2013 Apr 4.

PMID:
23592966
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions.

Bhattacharyya M, Vishveshwara S.

Mol Biosyst. 2011 Jul;7(7):2320-30. doi: 10.1039/c1mb05038a. Epub 2011 May 27.

PMID:
21617814
[PubMed - indexed for MEDLINE]
17.

A Bayesian method for construction of Markov models to describe dynamics on various time-scales.

Rains EK, Andersen HC.

J Chem Phys. 2010 Oct 14;133(14):144113. doi: 10.1063/1.3496438.

PMID:
20949993
[PubMed - indexed for MEDLINE]
18.

Everything you wanted to know about Markov State Models but were afraid to ask.

Pande VS, Beauchamp K, Bowman GR.

Methods. 2010 Sep;52(1):99-105. doi: 10.1016/j.ymeth.2010.06.002. Epub 2010 Jun 4. Review.

PMID:
20570730
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
23705683
[PubMed - indexed for MEDLINE]
20.

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
[PubMed - indexed for MEDLINE]

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