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Items: 1 to 20 of 165

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Structure and dynamics of end-to-end loop formation of the penta-peptide Cys-Ala-Gly-Gln-Trp in implicit solvents.

Yeh IC, Wallqvist A.

J Phys Chem B. 2009 Sep 10;113(36):12382-90. doi: 10.1021/jp904064z.

PMID:
19685925
3.

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

Seibert MM, Patriksson A, Hess B, van der Spoel D.

J Mol Biol. 2005 Nov 18;354(1):173-83.

PMID:
16236315
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The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage.

Linhananta A, Boer J, MacKay I.

J Chem Phys. 2005 Mar 15;122(11):114901.

PMID:
15836251
7.

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
8.

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

Marinelli F, Pietrucci F, Laio A, Piana S.

PLoS Comput Biol. 2009 Aug;5(8):e1000452. doi: 10.1371/journal.pcbi.1000452.

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Determination of ultrafast protein folding rates from loop formation dynamics.

Buscaglia M, Kubelka J, Eaton WA, Hofrichter J.

J Mol Biol. 2005 Apr 1;347(3):657-64.

PMID:
15755457
12.
13.

Experimental tests of villin subdomain folding simulations.

Kubelka J, Eaton WA, Hofrichter J.

J Mol Biol. 2003 Jun 13;329(4):625-30.

PMID:
12787664
14.

Rate of loop formation in peptides: a simulation study.

Feige MJ, Paci E.

J Mol Biol. 2008 Oct 3;382(2):556-65. doi: 10.1016/j.jmb.2008.07.011.

PMID:
18644378
15.

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
16.

Structure and dynamics of two beta-peptides in solution from molecular dynamics simulations validated against experiment.

Zagrovic B, Gattin Z, Lau JK, Huber M, van Gunsteren WF.

Eur Biophys J. 2008 Jul;37(6):903-12. doi: 10.1007/s00249-008-0307-y.

PMID:
18368403
17.

Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water.

Mohanty D, Elber R, Thirumalai D, Beglov D, Roux B.

J Mol Biol. 1997 Sep 26;272(3):423-42.

PMID:
9325101
19.

Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations.

Thukral L, Smith JC, Daidone I.

J Am Chem Soc. 2009 Dec 23;131(50):18147-52. doi: 10.1021/ja9064365.

PMID:
19919102
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