Unravelling the rules underlying protein-protein and protein-ligand interactions is a crucial step in understanding cell machinery. Peptide recognition modules (PRMs) are globular protein domains which focus their binding targets on short protein sequences and play a key role in the frame of protein-protein interactions. High-throughput techniques permit the whole proteome scanning of each domain, but they are characterized by a high incidence of false positives. In this context, there is a pressing need for the development of in silico experiments to validate experimental results and of computational tools for the inference of domain-peptide interactions.