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Results: 1 to 20 of 110

1.

Salt effects on hydrophobic-core formation in folding of a helical miniprotein studied by molecular dynamics simulations.

Yoda T, Sugita Y, Okamoto Y.

Proteins. 2014 Jun;82(6):933-43. doi: 10.1002/prot.24467. Epub 2013 Dec 6.

PMID:
24214490
[PubMed - indexed for MEDLINE]
2.

Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations.

Yoda T, Sugita Y, Okamoto Y.

Biophys J. 2010 Sep 8;99(5):1637-44. doi: 10.1016/j.bpj.2010.06.045.

PMID:
20816077
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Effect of subdomain interactions on methyl group dynamics in the hydrophobic core of villin headpiece protein.

Vugmeyster L, Do T, Ostrovsky D, Fu R.

Protein Sci. 2014 Feb;23(2):145-56. doi: 10.1002/pro.2398. Epub 2013 Dec 3.

PMID:
24243806
[PubMed - indexed for MEDLINE]
4.

Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure.

Lee IH, Kim SY, Lee J.

J Comput Chem. 2010 Jan 15;31(1):57-65. doi: 10.1002/jcc.21288.

PMID:
19412905
[PubMed - indexed for MEDLINE]
5.

Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations.

Lei H, Wu C, Liu H, Duan Y.

Proc Natl Acad Sci U S A. 2007 Mar 20;104(12):4925-30. Epub 2007 Mar 12.

PMID:
17360390
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid.

Mukherjee A, Bagchi B.

J Chem Phys. 2004 Jan 15;120(3):1602-12.

PMID:
15268287
[PubMed - indexed for MEDLINE]
7.

Microsecond scale replica exchange molecular dynamic simulation of villin headpiece: an insight into the folding landscape.

Jani V, Sonavane UB, Joshi R.

J Biomol Struct Dyn. 2011 Jun;28(6):845-60.

PMID:
21469746
[PubMed - indexed for MEDLINE]
8.

Reconciling the solution and X-ray structures of the villin headpiece helical subdomain: molecular dynamics simulations and double mutant cycles reveal a stabilizing cation-pi interaction.

Wickstrom L, Bi Y, Hornak V, Raleigh DP, Simmerling C.

Biochemistry. 2007 Mar 27;46(12):3624-34. Epub 2007 Mar 6.

PMID:
17338549
[PubMed - indexed for MEDLINE]
9.

A critical assessment of putative gatekeeper interactions in the villin headpiece helical subdomain.

Xiao S, Raleigh DP.

J Mol Biol. 2010 Aug 13;401(2):274-85. doi: 10.1016/j.jmb.2010.05.070. Epub 2010 Jun 4.

PMID:
20570680
[PubMed - indexed for MEDLINE]
10.

NMR characterization of a peptide model provides evidence for significant structure in the unfolded state of the villin headpiece helical subdomain.

Tang Y, Goger MJ, Raleigh DP.

Biochemistry. 2006 Jun 6;45(22):6940-6.

PMID:
16734429
[PubMed - indexed for MEDLINE]
11.

Ab initio folding of helix bundle proteins using molecular dynamics simulations.

Jang S, Kim E, Shin S, Pak Y.

J Am Chem Soc. 2003 Dec 3;125(48):14841-6.

PMID:
14640661
[PubMed - indexed for MEDLINE]
12.

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing.

Zagrovic B, Snow CD, Shirts MR, Pande VS.

J Mol Biol. 2002 Nov 8;323(5):927-37. Erratum in: J Mol Biol 2002 Dec 13;324(5):1051.

PMID:
12417204
[PubMed - indexed for MEDLINE]
13.

Large-scale context in protein folding: villin headpiece.

Fernández A, Shen MY, Colubri A, Sosnick TR, Berry RS, Freed KF.

Biochemistry. 2003 Jan 28;42(3):664-71.

PMID:
12534278
[PubMed - indexed for MEDLINE]
14.

Thermally induced protein unfolding probed by isotope-edited IR spectroscopy.

Wang L, Skinner JL.

J Phys Chem B. 2012 Aug 16;116(32):9627-34. doi: 10.1021/jp304613b. Epub 2012 Aug 1.

PMID:
22853174
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Free energy landscape of protein folding in water: explicit vs. implicit solvent.

Zhou R.

Proteins. 2003 Nov 1;53(2):148-61.

PMID:
14517967
[PubMed - indexed for MEDLINE]
16.

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.

Duan Y, Kollman PA.

Science. 1998 Oct 23;282(5389):740-4.

PMID:
9784131
[PubMed - indexed for MEDLINE]
Free Article
17.

Native like structure in the unfolded state of the villin headpiece helical subdomain, an ultrafast folding protein.

Meng W, Shan B, Tang Y, Raleigh DP.

Protein Sci. 2009 Aug;18(8):1692-701. doi: 10.1002/pro.152.

PMID:
19598233
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Protonation/deprotonation effects on the stability of the Trp-cage miniprotein.

Jimenez-Cruz CA, Makhatadze GI, Garcia AE.

Phys Chem Chem Phys. 2011 Oct 14;13(38):17056-63. doi: 10.1039/c1cp21193e. Epub 2011 Jul 20.

PMID:
21773639
[PubMed - indexed for MEDLINE]
19.

Analysis of core packing in a cooperatively folded miniature protein: the ultrafast folding villin headpiece helical subdomain.

Xiao S, Bi Y, Shan B, Raleigh DP.

Biochemistry. 2009 Jun 2;48(21):4607-16. doi: 10.1021/bi8021763.

PMID:
19354264
[PubMed - indexed for MEDLINE]
20.

Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces.

Wen EZ, Hsieh MJ, Kollman PA, Luo R.

J Mol Graph Model. 2004 May;22(5):415-24.

PMID:
15099837
[PubMed - indexed for MEDLINE]

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