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Items: 1 to 20 of 115

1.

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
2.

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
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.

A test of implicit solvent models on the folding simulation of the GB1 peptide.

Shao Q, Yang L, Gao YQ.

J Chem Phys. 2009 May 21;130(19):195104. doi: 10.1063/1.3132850.

PMID:
19466868
5.
6.

Folding thermodynamics of β-hairpins studied by replica-exchange molecular dynamics simulations.

Zerze GH, Uz B, Mittal J.

Proteins. 2015 Jul;83(7):1307-15. doi: 10.1002/prot.24827. Epub 2015 May 29.

PMID:
25973961
7.

Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.

Watts CR, Gregory A, Frisbie C, Lovas S.

Proteins. 2018 Mar;86(3):279-300. doi: 10.1002/prot.25439. Epub 2017 Dec 25.

PMID:
29235155
8.

Computational screening and selection of cyclic peptide hairpin mimetics by molecular simulation and kinetic network models.

Razavi AM, Wuest WM, Voelz VA.

J Chem Inf Model. 2014 May 27;54(5):1425-32. doi: 10.1021/ci500102y. Epub 2014 May 2.

PMID:
24754484
9.

Are AMBER Force Fields and Implicit Solvation Models Additive? A Folding Study with a Balanced Peptide Test Set.

Robinson MK, Monroe JI, Shell MS.

J Chem Theory Comput. 2016 Nov 8;12(11):5631-5642. Epub 2016 Oct 21.

PMID:
27731628
10.

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
11.

Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment.

Kent A, Jha AK, Fitzgerald JE, Freed KF.

J Phys Chem B. 2008 May 15;112(19):6175-86. doi: 10.1021/jp077099h. Epub 2008 Mar 19.

12.

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.

13.

A test on peptide stability of AMBER force fields with implicit solvation.

Shell MS, Ritterson R, Dill KA.

J Phys Chem B. 2008 Jun 5;112(22):6878-86. doi: 10.1021/jp800282x. Epub 2008 May 10.

14.
15.

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.

16.

Force field influences in beta-hairpin folding simulations.

Lwin TZ, Luo R.

Protein Sci. 2006 Nov;15(11):2642-55.

17.

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
18.

Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering.

Zhang T, Nguyen PH, Nasica-Labouze J, Mu Y, Derreumaux P.

J Phys Chem B. 2015 Jun 11;119(23):6941-51. doi: 10.1021/acs.jpcb.5b03381. Epub 2015 May 29.

PMID:
25985144
19.

Beta-hairpin folding by a model amyloid peptide in solution and at an interface.

Knecht V.

J Phys Chem B. 2008 Aug 7;112(31):9476-83. doi: 10.1021/jp8026513. Epub 2008 Jul 2.

PMID:
18593146
20.

How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory.

Deng NJ, Dai W, Levy RM.

J Phys Chem B. 2013 Oct 24;117(42):12787-99. doi: 10.1021/jp401962k. Epub 2013 Jun 13.

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