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Items: 1 to 20 of 137

1.

Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization.

Cerutti DS, Rice JE, Swope WC, Case DA.

J Phys Chem B. 2013 Feb 28;117(8):2328-38. doi: 10.1021/jp311851r. Epub 2013 Feb 18.

2.

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

Mobley DL, Dumont E, Chodera JD, Dill KA.

J Phys Chem B. 2007 Mar 8;111(9):2242-54. Epub 2007 Feb 10. Erratum in: J Phys Chem B. 2011 Feb 10;115(5):1329-32.

PMID:
17291029
3.

Communication: Quantum polarized fluctuating charge model: a practical method to include ligand polarizability in biomolecular simulations.

Kimura SR, Rajamani R, Langley DR.

J Chem Phys. 2011 Dec 21;135(23):231101. doi: 10.1063/1.3671638.

PMID:
22191857
4.

A new force field (ECEPP-05) for peptides, proteins, and organic molecules.

Arnautova YA, Jagielska A, Scheraga HA.

J Phys Chem B. 2006 Mar 16;110(10):5025-44.

PMID:
16526746
5.
6.

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P.

J Comput Chem. 2003 Dec;24(16):1999-2012.

PMID:
14531054
7.
9.

Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field.

Beckstein O, Fourrier A, Iorga BI.

J Comput Aided Mol Des. 2014 Mar;28(3):265-76. doi: 10.1007/s10822-014-9727-1. Epub 2014 Feb 21.

PMID:
24557853
10.

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.

11.

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.

Joung IS, Cheatham TE 3rd.

J Phys Chem B. 2008 Jul 31;112(30):9020-41. doi: 10.1021/jp8001614. Epub 2008 Jul 2.

12.

Electrostatic solvation free energy of amino acid side chain analogs: implications for the validity of electrostatic linear response in water.

Lin B, Pettitt BM.

J Comput Chem. 2011 Apr 15;32(5):878-85. doi: 10.1002/jcc.21668. Epub 2010 Oct 12.

PMID:
20941733
13.
14.

Alchemical prediction of hydration free energies for SAMPL.

Mobley DL, Liu S, Cerutti DS, Swope WC, Rice JE.

J Comput Aided Mol Des. 2012 May;26(5):551-62. doi: 10.1007/s10822-011-9528-8. Epub 2011 Dec 24.

15.

Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations.

Shaytan AK, Ivanov VA, Shaitan KV, Khokhlov AR.

J Comput Chem. 2010 Jan 15;31(1):204-16. doi: 10.1002/jcc.21267.

PMID:
19421988
16.

The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations.

Muddana HS, Sapra NV, Fenley AT, Gilson MK.

J Comput Aided Mol Des. 2014 Mar;28(3):277-87. doi: 10.1007/s10822-014-9714-6. Epub 2014 Jan 30.

17.

Predicting hydration Gibbs energies of alkyl-aromatics using molecular simulation: a comparison of current force fields and the development of a new parameter set for accurate solvation data.

Garrido NM, Jorge M, Queimada AJ, Gomes JR, Economou IG, Macedo EA.

Phys Chem Chem Phys. 2011 Oct 14;13(38):17384-94. doi: 10.1039/c1cp21245a. Epub 2011 Aug 31.

PMID:
21881653
18.

Calculation of the free energy of solvation for neutral analogs of amino acid side chains.

Villa A, Mark AE.

J Comput Chem. 2002 Apr 15;23(5):548-53.

PMID:
11948581
19.

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins.

Cerutti DS, Swope WC, Rice JE, Case DA.

J Chem Theory Comput. 2014 Oct 14;10(10):4515-4534. Epub 2014 Sep 18.

20.

Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent.

Li P, Roberts BP, Chakravorty DK, Merz KM Jr.

J Chem Theory Comput. 2013 Jun 11;9(6):2733-2748.

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