Patent ID: 8886505

Claim:
A computer-implemented method of predicting a protein-ligand docking structure, the method comprising: evaluating with a computer a protein-ligand docking structure by using a molecular mechanical energy-based scoring function; and reevaluating with said computer the protein-ligand docking structure by using a rescoring function obtained by incorporating a quantum mechanical factor with the molecular mechanical energy-based scoring function, selecting a most stable pose by performing a quantum mechanical calculation on a predefined quantum mechanical region with respect to the generated diverse poses and scoring energy values obtained by the quantum mechanical calculation, thereby predicting the protein-ligand docking structure, wherein the rescoring function obtained by incorporating the quantum mechanical factor is represented by the following equation (1): E=E QM +E MM +E QM/MM (1) wherein E QM is a quantum mechanical energy, E MM is a molecular mechanical energy, E QM/MM is an interaction energy between a quantum mechanical region and a molecular mechanical region and is represented by the following equation (2): E QM/MM =E Coulomb +E vdW + EQM/MM int.coor (2) wherein E coulomb is a Coulomb energy, E vdW is a van der Waals energy, and E QM/MM int.corr is an energy due to discrimination between a quantum mechanical region and a molecular mechanical region, and wherein the protein-ligand binding is hydrophobic binding that includes a π-stacking interaction, and wherein the ligand atoms and protein atoms of protein residues within 5 Å from the protein-ligand binding site are defined as the quantum mechanical region.