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Items: 1 to 20 of 88

1.

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements.

Beauchamp KA, Lin YS, Das R, Pande VS.

J Chem Theory Comput. 2012 Apr 10;8(4):1409-1414. Epub 2012 Mar 12.

2.

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.

3.

Critical Assessment of Current Force Fields. Short Peptide Test Case.

Vymětal J, Vondrášek J.

J Chem Theory Comput. 2013 Jan 8;9(1):441-51. doi: 10.1021/ct300794a. Epub 2012 Dec 14.

PMID:
26589046
4.

Improved side-chain torsion potentials for the Amber ff99SB protein force field.

Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE.

Proteins. 2010 Jun;78(8):1950-8. doi: 10.1002/prot.22711.

5.

The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development.

Jiang F, Han W, Wu YD.

Phys Chem Chem Phys. 2013 Mar 14;15(10):3413-28. doi: 10.1039/c2cp43633g.

PMID:
23385383
6.

Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics.

Pantelopulos GA, Mukherjee S, Voelz VA.

Proteins. 2015 Sep;83(9):1665-76. doi: 10.1002/prot.24852. Epub 2015 Jul 21.

PMID:
26138282
7.

Toward a predictive understanding of slow methyl group dynamics in proteins.

Long D, Li DW, Walter KF, Griesinger C, Brüschweiler R.

Biophys J. 2011 Aug 17;101(4):910-5. doi: 10.1016/j.bpj.2011.06.053.

8.

Conformational dynamics of HIV-1 protease: a comparative molecular dynamics simulation study with multiple amber force fields.

Meher BR, Kumar MV, Sharma S, Bandyopadhyay P.

J Bioinform Comput Biol. 2012 Dec;10(6):1250018. doi: 10.1142/S0219720012500187. Epub 2012 Jul 31.

PMID:
22845837
9.

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C.

J Chem Theory Comput. 2015 Aug 11;11(8):3696-713. doi: 10.1021/acs.jctc.5b00255. Epub 2015 Jul 23.

10.

Dynamic properties of force fields.

Vitalini F, Mey AS, Noé F, Keller BG.

J Chem Phys. 2015 Feb 28;142(8):084101. doi: 10.1063/1.4909549.

PMID:
25725706
11.

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
12.

Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles.

Verbaro D, Ghosh I, Nau WM, Schweitzer-Stenner R.

J Phys Chem B. 2010 Dec 30;114(51):17201-8. doi: 10.1021/jp109404r. Epub 2010 Dec 7.

PMID:
21138254
13.

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.

14.

Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.

Aliev AE, Courtier-Murias D.

J Phys Chem B. 2010 Sep 30;114(38):12358-75. doi: 10.1021/jp101581h. Erratum in: J Phys Chem B. 2012 Jul 12;116(27):7996.

PMID:
20825228
15.

Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models.

Xu L, Sun H, Li Y, Wang J, Hou T.

J Phys Chem B. 2013 Jul 18;117(28):8408-21. doi: 10.1021/jp404160y. Epub 2013 Jul 8.

PMID:
23789789
17.

The Dependence of Amyloid-β Dynamics on Protein Force Fields and Water Models.

Somavarapu AK, Kepp KP.

Chemphyschem. 2015 Oct 26;16(15):3278-89. doi: 10.1002/cphc.201500415. Epub 2015 Aug 19.

PMID:
26256268
18.

Residue-specific force field based on the protein coil library. RSFF1: modification of OPLS-AA/L.

Jiang F, Zhou CY, Wu YD.

J Phys Chem B. 2014 Jun 26;118(25):6983-98. doi: 10.1021/jp5017449. Epub 2014 May 28.

PMID:
24815738
19.

Bayesian energy landscape tilting: towards concordant models of molecular ensembles.

Beauchamp KA, Pande VS, Das R.

Biophys J. 2014 Mar 18;106(6):1381-90. doi: 10.1016/j.bpj.2014.02.009.

20.

Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.

Miller MS, Lay WK, Li S, Hacker WC, An J, Ren J, Elcock AH.

J Chem Theory Comput. 2017 Apr 11;13(4):1812-1826. doi: 10.1021/acs.jctc.6b01059. Epub 2017 Mar 27.

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