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Items: 1 to 20 of 109

1.

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
2.

Kinetic network models of tryptophan mutations in β-hairpins reveal the importance of non-native interactions.

Razavi AM, Voelz VA.

J Chem Theory Comput. 2015 Jun 9;11(6):2801-12. doi: 10.1021/acs.jctc.5b00088.

PMID:
26575573
3.

Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin.

Jimenez-Cruz CA, Garcia AE.

Phys Chem Chem Phys. 2014 Apr 14;16(14):6422-9. doi: 10.1039/c3cp54336f. Epub 2014 Jan 29.

PMID:
24472872
4.

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.

5.

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.

6.
7.

Folding thermodynamics of β-hairpins studied by replica-exchange molecular dynamics simulations.

Zerze GH, Uz B, Mittal J.

Proteins. 2015 Jul;83(7):1307-15. doi: 10.1002/prot.24827. Epub 2015 May 29.

PMID:
25973961
8.

Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding.

Zhou G, Voelz VA.

J Phys Chem B. 2016 Feb 11;120(5):926-35. doi: 10.1021/acs.jpcb.5b11767. Epub 2016 Feb 1.

PMID:
26769494
9.

Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding.

Radford IH, Fersht AR, Settanni G.

J Phys Chem B. 2011 Jun 9;115(22):7459-71. doi: 10.1021/jp112158w. Epub 2011 May 9.

10.

Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment.

Voelz VA, Jäger M, Yao S, Chen Y, Zhu L, Waldauer SA, Bowman GR, Friedrichs M, Bakajin O, Lapidus LJ, Weiss S, Pande VS.

J Am Chem Soc. 2012 Aug 1;134(30):12565-77. doi: 10.1021/ja302528z. Epub 2012 Jul 19.

11.

Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation.

Zanetti-Polzi L, Davis CM, Gruebele M, Dyer RB, Amadei A, Daidone I.

FEBS Lett. 2017 Oct;591(20):3265-3275. doi: 10.1002/1873-3468.12836. Epub 2017 Sep 21.

12.

Understanding the mechanism of beta-hairpin folding via phi-value analysis.

Du D, Tucker MJ, Gai F.

Biochemistry. 2006 Feb 28;45(8):2668-78.

PMID:
16489760
13.

Folding dynamics of the Trp-cage miniprotein: evidence for a native-like intermediate from combined time-resolved vibrational spectroscopy and molecular dynamics simulations.

Meuzelaar H, Marino KA, Huerta-Viga A, Panman MR, Smeenk LE, Kettelarij AJ, van Maarseveen JH, Timmerman P, Bolhuis PG, Woutersen S.

J Phys Chem B. 2013 Oct 3;117(39):11490-501. doi: 10.1021/jp404714c. Epub 2013 Sep 19.

PMID:
24050152
14.

Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.

de Groot BL, Daura X, Mark AE, Grubmüller H.

J Mol Biol. 2001 May 25;309(1):299-313.

PMID:
11491298
15.

Long range Trp-Trp interaction initiates the folding pathway of a pro-angiogenic β-hairpin peptide.

Diana D, De Rosa L, Palmieri M, Russomanno A, Russo L, La Rosa C, Milardi D, Colombo G, D'Andrea LD, Fattorusso R.

Sci Rep. 2015 Nov 25;5:16651. doi: 10.1038/srep16651.

16.

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
17.

Monitoring the folding kinetics of a β-hairpin by time-resolved IR spectroscopy in silico.

Daidone I, Thukral L, Smith JC, Amadei A.

J Phys Chem B. 2015 Apr 9;119(14):4849-56. doi: 10.1021/acs.jpcb.5b01477. Epub 2015 Mar 31.

PMID:
25777154
19.

Markov modeling of peptide folding in the presence of protein crowders.

Nilsson D, Mohanty S, Irbäck A.

J Chem Phys. 2018 Feb 7;148(5):055101. doi: 10.1063/1.5017031.

PMID:
29421894
20.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions.

Nedialkova LV, Amat MA, Kevrekidis IG, Hummer G.

J Chem Phys. 2014 Sep 21;141(11):114102. doi: 10.1063/1.4893963.

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