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Items: 1 to 20 of 148

1.

Coarse master equations for peptide folding dynamics.

Buchete NV, Hummer G.

J Phys Chem B. 2008 May 15;112(19):6057-69. doi: 10.1021/jp0761665. Epub 2008 Jan 31.

PMID:
18232681
2.

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
3.

Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers.

Leahy CT, Murphy RD, Hummer G, Rosta E, Buchete NV.

J Phys Chem Lett. 2016 Jul 21;7(14):2676-82. doi: 10.1021/acs.jpclett.6b00518. Epub 2016 Jun 30.

PMID:
27323250
4.
5.

Peptide folding kinetics from replica exchange molecular dynamics.

Buchete NV, Hummer G.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Mar;77(3 Pt 1):030902. Epub 2008 Mar 24.

PMID:
18517321
6.

Controlling protein molecular dynamics: how to accelerate folding while preserving the native state.

Jensen CH, Nerukh D, Glen RC.

J Chem Phys. 2008 Dec 14;129(22):225102. doi: 10.1063/1.3025888.

PMID:
19071948
7.

Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding.

Wong KB, Clarke J, Bond CJ, Neira JL, Freund SM, Fersht AR, Daggett V.

J Mol Biol. 2000 Mar 10;296(5):1257-82.

PMID:
10698632
8.

Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.

Sriraman S, Kevrekidis IG, Hummer G.

J Phys Chem B. 2005 Apr 14;109(14):6479-84.

PMID:
16851726
9.

Long-range electrostatic effects on peptide folding.

Aqvist J.

FEBS Lett. 1999 Sep 3;457(3):414-8.

10.

Folding Kinetics and Unfolded State Dynamics of the GB1 Hairpin from Molecular Simulation.

De Sancho D, Mittal J, Best RB.

J Chem Theory Comput. 2013 Mar 12;9(3):1743-53. doi: 10.1021/ct301033r. Epub 2013 Feb 7.

PMID:
26587632
11.

Helix nucleation kinetics from molecular simulations in explicit solvent.

Hummer G, García AE, Garde S.

Proteins. 2001 Jan 1;42(1):77-84.

PMID:
11093262
12.

Molecular dynamics simulation of folding of a short helical peptide with many charged residues.

Wei CC, Ho MH, Wang WH, Sun YC.

J Phys Chem B. 2005 Oct 27;109(42):19980-6.

PMID:
16853583
13.

Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature.

Mitsutake A, Takano H.

J Chem Phys. 2015 Sep 28;143(12):124111. doi: 10.1063/1.4931813.

PMID:
26429000
14.

Interplay between secondary and tertiary structure formation in protein folding cooperativity.

Bereau T, Bachmann M, Deserno M.

J Am Chem Soc. 2010 Sep 29;132(38):13129-31. doi: 10.1021/ja105206w.

15.

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
16.
18.

Identification of slow molecular order parameters for Markov model construction.

Pérez-Hernández G, Paul F, Giorgino T, De Fabritiis G, Noé F.

J Chem Phys. 2013 Jul 7;139(1):015102. doi: 10.1063/1.4811489.

PMID:
23822324
19.
20.

Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide.

Chowdhury S, Zhang W, Wu C, Xiong G, Duan Y.

Biopolymers. 2003 Jan;68(1):63-75.

PMID:
12579580

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