Prediction of protein–ligand complex structure by docking software guided by other complex structures

We developed a new scoring method that selects a protein–ligand complex structure with higher geometrical accuracy than the top-scoring complex structure, using the structural information of known protein–ligand complexes. To apply this method, one or more protein–ligand complex structures must be known for the target protein. A number of predicted structures were generated by the protein-compound docking program for a new ligand, and one of these structures, which showed the maximum overlap with the ligand coordinates of the known protein–ligand complex, was selected as the most probable complex structure.