Patent Document ID: 8538706
Application ID: 13270931
Patent Flag: 1

Claim One:
1. A method for determining an affinity score for a protein/ligand complex useful for estimating the affinity of the ligand for the protein, wherein said score is solely based on structural data and a force field function, the method comprising: (a) estimating desolvation energy for the ligand by a method comprising in silico simulation of immersion of one or more individual amino acid side-chains of the ligand; wherein the side-chains include at least one anchor residue, and are present in the ligand as amino acid model compounds in a solvent box filled with explicit water molecules, and applying the force field function to estimate the desolvation energy; (b) calculating ligand/protein complex interaction energy by a method comprising modeling with a computer a structural representation of the ligand placed in a binding site of the protein and applying the same force field function as used to estimate the desolvation energy in order to calculate the ligand/protein interaction energy; (c) calculating a conformational strain energy for the protein/ligand representation of step (b) by a method comprising applying the same force field function; and (d) subtracting the desolvation energy of step (a) and the conformational strain energy of step (c) from the ligand/protein interaction energy of step (b) to obtain said affinity score.