Abstract: The present invention provides an apparatus including a compound database which has been produced by extracting fingerprints of compound related to plural atoms in a compound for each candidate compound, characterized by extracting the fingerprints of compound of binding compounds that are already known to bind to family proteins having 3-dimensional structure that is identical or similar to that of target protein, together with the 3-dimensional coordinates that have been converted into the coordinate system of the target protein, to produce a fingerprint set of binding compound, and for a candidate compound stored in the compound database, computing the 3-dimensional structure of the candidate compound with respect to the target protein, so that the interaction score based on the root-mean-square deviation of a unit of fingerprint of compound calculated on the basis of the 3-dimensional coordinates of the fingerprint set of binding compound is optimized.

Abstract: An apparatus for processing 3-dimensional structure of protein includes a control unit and a storage unit, wherein the storage unit stores 3-dimensional structure information of protein, and the control unit predicts 3-dimensional structure information of protein after the mutation when an arbitrary amino acid residue A in the 3-dimensional structure information of protein stored in the storage unit is mutated into another amino acid residue a, thereof from the 3-dimensional structure information of protein before and after the mutation, collects the amino acid residue A, the amino acid residue a, environment information P, and environment information p, which are related to each other, as information on environmental change, when the environment information P around the amino acid residue A before the mutation changes to the environment information p around the amino acid residue a after the mutation, thereby storing information on the environmental change in the storage unit.