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

E. V. Sobolev ; D. A. Tikhonov ; H. Fridman ; T. N. Truong

Matematičeskaâ biologiâ i bioinformatika, Tome 5 (2010) no. 2, pp. 98-113.

Résumé

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.

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