Abstract: A method and apparatus are disclosed for automated detection of possible protein and nucleic acid targets of a given drug. The advantage of this invention over existing methods is its unique capability of drug target detection. In contrast, existing computer methods are designed for screening multiple chemical compounds to find one or more compounds that can bind to a protein or nucleic acid, and they are not capable of finding drug targets. Potential applications of this method and apparatus include unknown target or secondary target identification for drugs, lead compounds, and natural products. It may also potentially facilitate the prediction of drug side-effect and toxicity based on the analysis of function of identified protein or nucleic acid targets. A ligand-biomolecule inverse-docking algorithm is disclosed to flexibly dock a ligand to multiple entries in a biomolecular cavity database.