Abstract: The invention concerns a method for generating lead molecules capable of interacting with a target protein of interest. In particular, the method identifies the binding sites of proteins, characterises the types of atomic interactions available within those binding sites, and uses this information as a means of identifying lead molecules predicted to be capable of interaction with these proteins. The method includes the steps of predicting the configuration of a binding site in said target protein, dividing the binding site into a plurality of grid points, generating a three-dimensional density map of preferred atom-atom contact distributions in the binding site and generating a molecular interaction search template from said three-dimensional density map.