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Items: 1 to 20 of 114

1.

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields.

Lin B, Lopes PE, Roux B, MacKerell AD Jr.

J Chem Phys. 2013 Aug 28;139(8):084509. doi: 10.1063/1.4818731.

2.

A comparative Kirkwood-Buff study of aqueous methanol solutions modeled by the CHARMM additive and Drude polarizable force fields.

Lin B, He X, MacKerell AD Jr.

J Phys Chem B. 2013 Sep 12;117(36):10572-80. doi: 10.1021/jp4061889. Epub 2013 Aug 29.

4.
5.

Studies of enthalpy-entropy compensation, partial entropies, and Kirkwood-Buff integrals for aqueous solutions of glycine, L-leucine, and glycylglycine at 298.15 K.

Kurhe DN, Dagade DH, Jadhav JP, Govindwar SP, Patil KJ.

J Phys Chem B. 2009 Dec 31;113(52):16612-21. doi: 10.1021/jp9078585.

PMID:
19924870
6.

A Kirkwood-Buff force field for the aromatic amino acids.

Ploetz EA, Smith PE.

Phys Chem Chem Phys. 2011 Oct 28;13(40):18154-67. doi: 10.1039/c1cp21883b. Epub 2011 Sep 19.

7.

A Kirkwood-Buff derived force field for amides.

Kang M, Smith PE.

J Comput Chem. 2006 Oct;27(13):1477-85.

PMID:
16823811
8.

Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator.

He X, Lopes PE, Mackerell AD Jr.

Biopolymers. 2013 Oct;99(10):724-38. doi: 10.1002/bip.22286.

9.

Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.

Savelyev A, MacKerell AD Jr.

J Phys Chem B. 2014 Jun 19;118(24):6742-57. doi: 10.1021/jp503469s. Epub 2014 Jun 9.

10.
11.

Kirkwood-Buff derived force field for alkali chlorides in simple point charge water.

Klasczyk B, Knecht V.

J Chem Phys. 2010 Jan 14;132(2):024109. doi: 10.1063/1.3273903.

PMID:
20095665
12.

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.

Vanommeslaeghe K, MacKerell AD Jr.

Biochim Biophys Acta. 2015 May;1850(5):861-71. doi: 10.1016/j.bbagen.2014.08.004. Epub 2014 Aug 19. Review.

13.

Understanding the dielectric properties of liquid amides from a polarizable force field.

Harder E, Anisimov VM, Whitfield T, MacKerell AD Jr, Roux B.

J Phys Chem B. 2008 Mar 20;112(11):3509-21. doi: 10.1021/jp709729d. Epub 2008 Feb 27.

14.

Structural and technical details of the Kirkwood-Buff integrals from the optimization of ionic force fields: focus on fluorides.

Fyta M.

Eur Phys J E Soft Matter. 2012 Mar;35(3):1-12. doi: 10.1140/epje/i2012-12021-2. Epub 2012 Mar 22.

PMID:
22434150
15.

Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model.

Baker CM, Anisimov VM, MacKerell AD Jr.

J Phys Chem B. 2011 Jan 27;115(3):580-96. doi: 10.1021/jp1092338. Epub 2010 Dec 17.

16.

All-atom polarizable force field for DNA based on the classical Drude oscillator model.

Savelyev A, MacKerell AD Jr.

J Comput Chem. 2014 Jun 15;35(16):1219-39. doi: 10.1002/jcc.23611. Epub 2014 Apr 18.

17.

Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers.

Baker CM, Mackerell AD Jr.

J Mol Model. 2010 Mar;16(3):567-76. doi: 10.1007/s00894-009-0572-4. Epub 2009 Aug 25.

18.

Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator.

Patel DS, He X, MacKerell AD Jr.

J Phys Chem B. 2015 Jan 22;119(3):637-52. doi: 10.1021/jp412696m. Epub 2014 Feb 24.

19.

Ion specificity at the peptide bond: molecular dynamics simulations of N-methylacetamide in aqueous salt solutions.

Heyda J, Vincent JC, Tobias DJ, Dzubiella J, Jungwirth P.

J Phys Chem B. 2010 Jan 21;114(2):1213-20. doi: 10.1021/jp910953w.

PMID:
20038160

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