Methods and systems for estimating binding affinity

Details Methods and systems for estimating binding affinity Methods and systems for estimating binding affinity

G - Physics

01

N

G01N 33/53 (2006.01) G01N 33/483 (2006.01)

Patent

CA 2346588

This application discloses methods and systems of predicting binding affinity between a ligand and a receptor. In one embodiment, the predicted binding affinity (pK i) is determined by at least using a formula pK i = C0 + C1 * vdW + C2 * Att_pol + C3 * (Att_pol * Att_pol + Rep_pol * Rep_pol). vdW represents the van der Waals interaction energy between the ligand and the receptor. Att_pol represents the surface area of the ligand forming complimentary polar interactions with the receptor. Rep_pol represents the surface area of the ligand forming uncomplimentary polar interactions with the receptor. This application also discloses an improved process of calculating linear interpolation of grid-based vdW energy. A first non-linear function is transformed into a less non-linear second non-linear function to reduce the error in linear interpolation. A trilinear interpolation process is applied to the second non-linear function. The value obtained is reverse transformed to produce an estimated vdW energy.

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