Patent ID: 7386400

Claim:
A method of analyzing three-dimensional structures of a predetermined amino acid sequence probe and a protein molecule target, wherein the predetermined amino acid sequence probe includes a first structure expressed by three-dimensional coordinates of elements belonging to a first point set and the protein molecule target includes a second structure expressed by three-dimensional coordinates of elements belonging to a second point set, to determine a degree of similarity between the three dimensional structure of the predetermined amino acid sequence probe represented by the three-dimensional coordinates of the elements belonging to the first point set and the three-dimensional structure of the protein molecule target represented by the three-dimensional coordinates of elements belonging to the second point set, comprising: generating, by a superposition calculating unit, a combination of correspondences comprising generating the combination by generating a decision tree having at least one retrieval path, the decision tree being based on determining that a point is a candidate if an attribute of an element of the first point set includes a type of an atom, an atomic group, a molecule, a hydrophilic property, a hydrophobic property, or a positive or negative charge that coincides with an attribute of an element of the second point set, and based on minimized root mean square distance (rmsd) values between the first and second point sets, setting a predetermined threshold value and pruning a retrieval path if an rmsd value of a point is greater than the predetermined threshold value to generate a restricted set of candidates, thereby refining the elements of the first and second point sets based on coinciding attributes of the elements of the first and second point sets to provide a first subset and a second subset, respectively; calculating, by the superposition calculating unit, a root mean square distance between the elements belonging to the first subset of the first point set relating to the elements belonging to the second subset of the second point set in the generated combination of correspondence; determining, by the superposition calculating unit, based on the generated combination of correspondence and minimizing root mean square distance values, similar portions of the three dimensional structure of the predetermined amino acid sequence probe represented by the three-dimensional coordinates of the elements belonging to the first point set and the three-dimensional structure of the protein molecule target represented by the three-dimensional coordinates of elements belonging to the second point set; and displaying, by a graphic display unit, the three-dimensional structures of the predetermined amino acid sequence probe and the protein molecule target in an overlapped manner based on the generated combination of correspondence.