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Items: 1 to 20 of 101

1.

Modeling the mechanism of CLN025 beta-hairpin formation.

McKiernan KA, Husic BE, Pande VS.

J Chem Phys. 2017 Sep 14;147(10):104107. doi: 10.1063/1.4993207.

2.

Raising the speed limit for β-hairpin formation.

Davis CM, Xiao S, Raleigh DP, Dyer RB.

J Am Chem Soc. 2012 Sep 5;134(35):14476-82. doi: 10.1021/ja3046734. Epub 2012 Aug 21.

3.

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations.

Cino EA, Choy WY, Karttunen M.

J Chem Theory Comput. 2012 Aug 14;8(8):2725-2740. Epub 2012 Jun 19.

4.

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
5.

Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein.

Zhao GJ, Cheng CL.

Amino Acids. 2012 Aug;43(2):557-65. doi: 10.1007/s00726-011-1150-5. Epub 2011 Nov 24.

PMID:
22113644
6.

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
8.

Low-mass molecular dynamics simulation: a simple and generic technique to enhance configurational sampling.

Pang YP.

Biochem Biophys Res Commun. 2014 Sep 26;452(3):588-92. doi: 10.1016/j.bbrc.2014.08.119. Epub 2014 Aug 30.

9.

An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β-Hairpin, and Intrinsically Disordered Peptides.

Maffucci I, Contini A.

J Chem Theory Comput. 2016 Feb 9;12(2):714-27. doi: 10.1021/acs.jctc.5b01211. Epub 2016 Jan 27.

PMID:
26784558
10.

A fully atomistic computer simulation study of cold denaturation of a β-hairpin.

Yang C, Jang S, Pak Y.

Nat Commun. 2014 Dec 15;5:5773. doi: 10.1038/ncomms6773.

PMID:
25502835
11.
12.

The CLN025 decapeptide retains a β-hairpin conformation in urea and guanidinium chloride.

Hatfield MP, Murphy RF, Lovas S.

J Phys Chem B. 2011 May 5;115(17):4971-81. doi: 10.1021/jp111076j. Epub 2011 Apr 11.

13.

FF12MC: A revised AMBER forcefield and new protein simulation protocol.

Pang YP.

Proteins. 2016 Oct;84(10):1490-516. doi: 10.1002/prot.25094. Epub 2016 Jul 21.

14.

Structure change of β-hairpin induced by turn optimization: an enhanced sampling molecular dynamics simulation study.

Shao Q, Yang L, Gao YQ.

J Chem Phys. 2011 Dec 21;135(23):235104. doi: 10.1063/1.3668288.

PMID:
22191904
15.

Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method.

Harada R, Kitao A.

J Phys Chem B. 2011 Jul 14;115(27):8806-12. doi: 10.1021/jp2008623. Epub 2011 Jun 22.

PMID:
21648487
16.

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
17.

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
18.

The mechanism of beta-hairpin formation.

Dyer RB, Maness SJ, Peterson ES, Franzen S, Fesinmeyer RM, Andersen NH.

Biochemistry. 2004 Sep 14;43(36):11560-6.

PMID:
15350142
19.

Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields.

Chen W, Shi C, MacKerell AD Jr, Shen J.

J Phys Chem B. 2015 Jun 25;119(25):7902-10. doi: 10.1021/acs.jpcb.5b02290. Epub 2015 Jun 15.

20.

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

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