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Items: 1 to 20 of 122

1.

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
2.

Effects of a mutation on the folding mechanism of a beta-hairpin.

Juraszek J, Bolhuis PG.

J Phys Chem B. 2009 Dec 17;113(50):16184-96. doi: 10.1021/jp904468q.

PMID:
19924848
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.

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
5.

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
6.
7.

Computational and Experimental Evaluation of Designed β-Cap Hairpins Using Molecular Simulations and Kinetic Network Models.

Ge Y, Kier BL, Andersen NH, Voelz VA.

J Chem Inf Model. 2017 Jul 24;57(7):1609-1620. doi: 10.1021/acs.jcim.7b00132. Epub 2017 Jun 29.

PMID:
28614661
8.

Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations.

Kannan S, Zacharias M.

PLoS One. 2014 Feb 7;9(2):e88383. doi: 10.1371/journal.pone.0088383. eCollection 2014.

9.

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
10.
11.

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.

12.

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.

13.

Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar.

Baxa MC, Yu W, Adhikari AN, Ge L, Xia Z, Zhou R, Freed KF, Sosnick TR.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8302-7. doi: 10.1073/pnas.1503613112. Epub 2015 Jun 22.

14.

The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations.

Snow CD, Zagrovic B, Pande VS.

J Am Chem Soc. 2002 Dec 11;124(49):14548-9.

PMID:
12465960
15.

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
16.

Complex pathways in folding of protein G explored by simulation and experiment.

Lapidus LJ, Acharya S, Schwantes CR, Wu L, Shukla D, King M, DeCamp SJ, Pande VS.

Biophys J. 2014 Aug 19;107(4):947-55. doi: 10.1016/j.bpj.2014.06.037.

17.

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.

18.

A lattice protein with an amyloidogenic latent state: stability and folding kinetics.

Palyanov AY, Krivov SV, Karplus M, Chekmarev SF.

J Phys Chem B. 2007 Mar 15;111(10):2675-87. Epub 2007 Feb 22.

PMID:
17315918
20.

Intermediates and transition states in protein folding.

Thirumalai D, Klimov DK.

Methods Mol Biol. 2007;350:277-303.

PMID:
16957328

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