Levy RM - Search Results

1

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

Levy RM, Gallicchio E. Levy RM, et al. Annu Rev Phys Chem. 1998;49:531-67. doi: 10.1146/annurev.physchem.49.1.531. Annu Rev Phys Chem. 1998. PMID: 9933909 Review.

2

Intrinsic pKas of ionizable residues in proteins: an explicit solvent calculation for lysozyme.

Del Buono GS, Figueirido FE, Levy RM. Del Buono GS, et al. Among authors: levy rm. Proteins. 1994 Sep;20(1):85-97. doi: 10.1002/prot.340200109. Proteins. 1994. PMID: 7824525

3

Molecular mechanics and electrostatic effects.

Figueirido F, Del Buono GS, Levy RM. Figueirido F, et al. Among authors: levy rm. Biophys Chem. 1994 Aug;51(2-3):235-41. doi: 10.1016/0301-4622(94)00044-1. Biophys Chem. 1994. PMID: 7919034

4

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

Gallicchio E, Zhang LY, Levy RM. Gallicchio E, et al. Among authors: levy rm. J Comput Chem. 2002 Apr 15;23(5):517-29. doi: 10.1002/jcc.10045. J Comput Chem. 2002. PMID: 11948578

5

Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model.

Felts AK, Gallicchio E, Wallqvist A, Levy RM. Felts AK, et al. Among authors: levy rm. Proteins. 2002 Aug 1;48(2):404-22. doi: 10.1002/prot.10171. Proteins. 2002. PMID: 12112706

6

On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.

Levy RM, Zhang LY, Gallicchio E, Felts AK. Levy RM, et al. J Am Chem Soc. 2003 Aug 6;125(31):9523-30. doi: 10.1021/ja029833a. J Am Chem Soc. 2003. PMID: 12889983

7

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

Gallicchio E, Levy RM. Gallicchio E, et al. Among authors: levy rm. J Comput Chem. 2004 Mar;25(4):479-99. doi: 10.1002/jcc.10400. J Comput Chem. 2004. PMID: 14735568

8

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model.

Felts AK, Harano Y, Gallicchio E, Levy RM. Felts AK, et al. Among authors: levy rm. Proteins. 2004 Aug 1;56(2):310-21. doi: 10.1002/prot.20104. Proteins. 2004. PMID: 15211514

9

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

Andrec M, Felts AK, Gallicchio E, Levy RM. Andrec M, et al. Among authors: levy rm. Proc Natl Acad Sci U S A. 2005 May 10;102(19):6801-6. doi: 10.1073/pnas.0408970102. Epub 2005 Mar 30. Proc Natl Acad Sci U S A. 2005. PMID: 15800044 Free PMC article.

10

Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein.

Ravindranathan KP, Gallicchio E, Levy RM. Ravindranathan KP, et al. Among authors: levy rm. J Mol Biol. 2005 Oct 14;353(1):196-210. doi: 10.1016/j.jmb.2005.08.009. J Mol Biol. 2005. PMID: 16157349

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