Application of the RISM method to estimate the relative gibbs free energies of 4${}'$,6-diamidino-2-phenylindole binding within the minor groove of a DNA along simulation trajectory
Abstract:
The efficient parallel algorithm for solving RISM equations in infinity dilution limit and estimate of solvation free energy was applied to study the relative binding energies of sequence-specific binding modes of 4${}'$,6-diamidino-2-phenylindole (DAPI) within the minor groove of a DNA duplex. The speedy implementation allows solvation free energies to be calculated at all points along a given simulation trajectory, leading to a more accurate representation of the solute than in the usual RISM approach considering the solute molecule as frozen.
Key words:thermodynamics, solvation of macromolecule, Gibbs free energy, integral equations of theory of liquids, RISM, DNA.