With the advent of domain interaction networks derived from 3D structures and experimentally determined large-scale protein interaction networks a number of interesting questions arise: Are interaction interfaces more conserved than the rest of the surfaces? Can the structure of protein interaction networks be linked to underlying domain interactions? Can motifs derived from domain interactions predict protein interactions? Can viral domains mimick native human protein interaction interfaces? There is an intricate relationship between domain-domain and protein-protein interactions, whose understanding helps to answer the above questions. In the talk, I will review how to construct networks derived from structural domains and how to complement large-experimental protein interaction networks with interactions extracted from literature. I will shed light onto the structure of these networks, how to identify functional modules, and how to predict interactions. The discussed techniques will be used to identify candidate targets in pancreas cancer and will show how viruses interfere with the apoptotic programme of their hosts.