With compounds for drugs, agricultural chemicals, etc., the invention provides a novel method for superposing molecular structures of those compounds. A method for superposing molecular structures of compounds characterized in that, upon superposing the molecular structures of a plurality of compounds, (1) the characteristic groups (atoms) of compounds are roughly divided into four types of hydrophobicity (aliphatic chain/ring, aromatic ring and halogen), hydrogen-bonding donor, hydrogen-bonding acceptor and hydrogen-bonding donor/acceptor, (2) a molecule of compound with large radius of inertia calculated from constituting characteristic groups (atoms) is fixed, superposition is performed among a set of characteristic groups (atoms) with the same nature between two molecules of compounds, and operations of translation and rotation are performed in its neighborhood, (3) when causing the superposition of characteristic groups (atoms) between molecules of compounds by the operations of translation and rotation in (2), a score is given depending on the combination between respective characteristic groups (atoms), (4) scores of superposition are summed up, and (5) said operations of (2) through (4) are repeated to find out an orientation that acquires the highest score value.