Abstract: The present invention relates to a method for identifying compounds comprising the steps of: (a) providing a set of compounds; (b) optionally selecting a sub-set from the set of compounds based on one or more specific compound properties; (c) generating a 3D structure of each of the compounds provided and/or selected in step (a) or (b); (d) encoding each 3D structure; (e) providing at least one known compound having at least one desired property and/or providing a target molecule; (f) encoding the 3D structure of (each of) the known compound(s) provided in step (e) and/or the active site of the target molecule provided in step (e); (g) comparing said encoded 3D structure(s) of step (d) with the encoded 3D structure(s) of step (f); and (h) selecting all compounds falling within a specified similarity range.