The present invention addresses the problem of providing a binding site identification device, a binding site identification method and a binding site identification program which are capable of identifying a suitable binding site, even when using a low molecular weight binding substance. According to one embodiment of the present invention, on the basis of the three-dimensional structure of a target substance, and experiment results pertaining to the numbers of substances of interest deemed to participate in binding, a location deemed to correspond to the experiment results with regard to the numbers of the substances of interest is found from a search space including the surface of the target substance, and a binding site is identified on the basis of the found location.
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