A method of predicting a biological function of one or more query proteins having predetermined or predictable steric structures using a three-dimensional structure database comprising: (a) selecting at least one bio-active compound capable of binding to the query protein as ligand candidates from the database based on the capability of complex formation between the query protein and bio-active compound; and (b) predicting that a biological function of the query protein are identical or similar to the biological functions of proteins with predetermined biological functions to which the ligand candidates bind, wherein the database comprises the structure of at least one bio-active compound which binds to proteins with predetermined biological functions.