Accelrys, Inc.

Paul Kirchhoff

Marvin Waldman

Cherayathumadom M Venkatachalam

Xiaohui Jiang

Methods and systems of predicting binding affinity between a ligand and a receptor. In one embodiment, the predicted binding affinity (pKj) is determined by at least using a formula pKj&equals;C0&plus;C1*vdW&plus;C2*Att_pol&plus;C3*(Att_pol*Att_pol&plus;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. 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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Ann Arbor, MI, United States of America

Paul Kirchhoff