Marvin Waldman - San Diego CA, US Paul Kirchhoff - Ann Arbor MI, US Xiaohui Jiang - San Diego CA, US
International Classification:
G06F019/00 G01N033/48 G01N033/50
US Classification:
702/019000
Abstract:
This application discloses methods and systems of predicting binding affinity between a ligand and a receptor. In one embodiment, the predicted binding affinity (pK) is determined by at least using a formula pK=C+C*vdW+C*Att_pol+C*(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.