Patent ID: 7739091

Claim:
A method, for execution on a computing device, of predicting the binding affinity between a first molecular entity and a second molecular entity, wherein the first molecular entity or the second molecular entity comprises a protein or a peptide, comprising the steps of: (1) calculating the free energy of binding ΔG bind between said first molecular entity and said second molecular entity according to the following equation: ΔG bind =−0.82 Δ X +/− +0.064Δ X c/s −0.6 X sb −0.93 X hb −0.0007 X gap −0.06Δ X tor −0.36 wherein ΔG bind is given by a linear combination consisting of seven terms including a constant and six terms each having a coefficient and a distinct one of six parameters ΔX +/− , ΔX c/s , X sb , X hb , X gap , ΔX tor , where X +/− is the total number of exposed charged groups; X c/s is the total number of exposed hydrophobic groups; X sb is the total number of salt bridges; X hb is the total number of hydrogen bonds; X gap is the gap volume at the interface of said first molecular entity and said second molecular entity; X tor is the total number of exposed side chain torsions; and wherein Δ refers to the difference between the bound and unbound states; (2) evaluating said free energy of binding to predict the binding affinity between said first molecular entity and said second molecular entity; and (3) outputting said evaluation to a user in a user-readable format; wherein said calculating, said evaluating and said outputting steps are performed with the computing device, the computing device being configured to perform said steps.