Abstract: When the interaction of a compound is predicted by using a computer, a technique to highly precisely design a compound having a novel structure has been required. A compound designing device is provided which includes an input unit configured to receive, at least about one or more query proteins, one or more pieces of query protein information corresponding to the one or more query proteins; and a processing unit configured to perform steps of (a) generating one or more pieces of compound information, (b) computing a score indicating interaction potential between a compound corresponding to the compound information and each of the one or more query proteins, (c) updating the compound information by an optimization method with reference to the score computed at step (b) such that the interaction potential increases, and (d) repeating steps (b) and (c) a plurality of times.