Molecular dynamics free-energy perturbation

S. Miyamoto and P. A. Kollman. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins, 16 226-245, 1993. 

Miyamoto S and P A Kollman 1993a. Absolute and Relative Binding Tree Energy Calculations of the Interaction of Biotin and its Analogues with Streptavidin Using Molecular Dynamics/Free Energy Perturbation Approaches. Proteins Structure, Function and Genetics 16 226-245. 

S Hirono, PA Kollman. Calculation of the relative binding free energy of 2 -GMP and 2 -AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches. J Mol Biol 212 197-209, 1990. 

Ding YB, Bernardo DN, Kroghjespersen K, Levy RM (1995) Solvation free-energies of small amides and amines from molecular-dynamics free-energy perturbation simulations using pairwise additive and many-body polarizable potentials. J Phys Chem 99(29) 11575—11583... 

Chipot, C. Millot, C. Maigret, B. Kollman, P. A., Molecular dynamics free energy perturbation calculations. Influence of nonbonded parameters on the free energy of hydration of charged and neutral species, J. Phys. Chem. 1994, 98,11362-11372... 

Molecular dynamics free-energy perturbation simulations utilizing the empirical valence bond model have been used to study the catalytic action of -cyclodextrin in ester hydrolysis. Reaction routes for nucleophilic attack on m-f-butylphenyl acetate (225) by the secondary alkoxide ions 0(2) and 0(3) of cyclodextrin giving the R and S stereoisomers of ester tetrahedral intermediate were examined. Only the reaction path leading to the S isomer at 0(2) shows an activation barrier that is lower (by about 3kcal mol ) than the barrier for the corresponding reference reaction in water. The calculated rate acceleration was in excellent agreement with experimental data. ... 

Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials. 

Hirono, S. and Kollman, P.A. (1991) Relative binding free energy calculations of inhibitors to two mutants (Glu46 — Ala/Gin) of ribonuclease T1 using molecular dynamics/free energy perturbation approaches, Prot. Eng. 4, 233-243. 

A molecular dynamics free-energy perturbation simulation (121) comparing the phosphonamidate and phosphonate in solution and in the enzyme... 

Roux, B., Nina, M., Pomes, R., Smith, J.C. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel a molecular dynamics free energy perturbation study, Biophys. J. 1996, 71(2), 670-81. 

P. L. Cummins, K. Ramnarayan, U. C. Singh, andj. E. Gready,/. Am. Ghem. Soc., 113,8247 (1991). Molecular Dynamics Free Energy Perturbation Study on the Relative Affinities of Binding of Reduced and Oxidized NADP to Dihydrofolate Reductase. 

Validation of the OPLS2.0 force field includes comparison to quantum mechanical energy profiles and experimental solvation free energies. For the latter, we performed explicit solvent molecular dynamics free energy perturbation simulations on a set of 239 diverse small molecules [80]. Compared with other popular force fields... 

C. Chipot, C. Millot, B. Maigret, and P. A. Kollman, /. Phys. Chem., 98, 11362 (1994), Molecular Dynamics Free Energy Perturbation Calculations Influence of Nonbonded Parameters on the Free Energy of Hydration of Charged and Neutral Species. 

S. Hirono and P. A. Kollman, J. Mol. Biol., 212, 197 (1990). Calculation of the Relative Binding Free Energy of 2 GMP and 2 AMP to Ribonuclease Using Molecular Dynamics/ Free Energy Perturbation Approaches. 

S. Hirono and R A. KoUman, Protein Eng., 4, 233 (1991). Relative Binding Free Energy Calculations of Inhibitors to Two Mutants (Glu46 - Ala/GIn) of Ribonudease T Using Molecular Dynamics/Free Energy Perturbation Approaches. 

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