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Items: 1 to 20 of 247

1.

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
2.

ETNA: equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations.

Muff S, Caflisch A.

J Phys Chem B. 2009 Mar 12;113(10):3218-26. doi: 10.1021/jp807261h.

PMID:
19231819
3.

Protein folding pathways from replica exchange simulations and a kinetic network model.

Andrec M, Felts AK, Gallicchio E, Levy RM.

Proc Natl Acad Sci U S A. 2005 May 10;102(19):6801-6. Epub 2005 Mar 30.

4.
5.

Simulating replica exchange simulations of protein folding with a kinetic network model.

Zheng W, Andrec M, Gallicchio E, Levy RM.

Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15340-5. Epub 2007 Sep 18.

6.

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. Epub 2005 Sep 29.

PMID:
16236315
8.
9.

Error and efficiency of replica exchange molecular dynamics simulations.

Rosta E, Hummer G.

J Chem Phys. 2009 Oct 28;131(16):165102. doi: 10.1063/1.3249608.

10.

Convergence of replica exchange molecular dynamics.

Zhang W, Wu C, Duan Y.

J Chem Phys. 2005 Oct 15;123(15):154105.

PMID:
16252940
11.
12.
13.

Exploring the helix-coil transition via all-atom equilibrium ensemble simulations.

Sorin EJ, Pande VS.

Biophys J. 2005 Apr;88(4):2472-93. Epub 2005 Jan 21.

14.

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
15.

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
16.

Reversible folding simulation by hybrid Hamiltonian replica exchange.

Xu W, Lai T, Yang Y, Mu Y.

J Chem Phys. 2008 May 7;128(17):175105. doi: 10.1063/1.2911693.

PMID:
18465944
17.
18.

Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins.

Pitera JW, Swope W.

Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7587-92. Epub 2003 Jun 13.

19.
20.

Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide.

Cavalli A, Vendruscolo M, Paci E.

Biophys J. 2005 May;88(5):3158-66. Epub 2005 Mar 4.

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