Structure-based drug design (SBDD) is one of the attractive and promising methods in drug discovery. In this study, we developed a software program predicting the binding site and the binding mode of ligands against a target protein for SBDD. The prediction method is based on the calculation of the hydrophobic potential energies around a target protein because the hydrophobic interaction is considered to be an important driving force in molecular recognition. Our program was tested with exemplifying 5 kinds of proteins, and was demonstrated to correctly predict the binding site and the binding mode of ligands seen in the experimentally determined structures for the protein-ligand complex. [DOI: 10.1380/ejssnt.2008.241]