Objective sequence data (10) which is primary sequence information on an objective protein is entered in an interaction portion predicting device by the user. A secondary structure prediction simulation of the objective sequence data (10) entered through secondary structure prediction programs (20a to 20d) for predicting the secondary structure of the protein from the primary sequence information on the protein is executed. The results (30a to 30d) of the secondary structure predictions through the secondary structure prediction programs (20a to 20d) are compared with one another (60). On the basis of the comparison results, the frustration of a local portion of the primary sequence information of the objective protein is calculated (70). From the calculated frustration of the local portion, the interaction portion of the objective protein is predicted (80).
