Helmholtz free energy of the Lennard-Jones (LJ) crystal is calculated accurately while accounting for both the anharmonicity of atomic vibrations and the pair and triple correlations in displacements of the atoms from their lattice sites. We discuss the problem of the quantitative theoretical prediction of the absolute free energy for classical highly anharmonic solids. The paradigm used is able to rank two inhibitors having the maximum difference of âˆ❁.5 kcal/mol in absolute binding free energies.Ībsolute Helmholtz free energy of highly anharmonic crystals: theory vs Monte Carlo. Theoretical binding affinities are in good correlation with experimental data, with R = 0.89. The calculated free energy difference terms help clarifying the nature of the binding. The absolute binding free energy of an inhibitor to HIV-1 Protease (PR) was determined throughout evaluation of the non-bonded interaction energy difference between the two bound and unbound states of the inhibitor and surrounding molecules by the fast pulling of ligand (FPL) process using non-equilibrium molecular dynamics (NEMD) simulations. Ngo, Son Tung Nguyen, Minh Tung Nguyen, Minh Tho Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations
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