Protein interactions are of biological interest because they orchestrate a number of cellular processes such as metabolic pathways and immunological recognition. Domains are the building blocks of proteins, therefore, proteins are assumed to interact as a result of their interacting domains. Many domain-based models for protein interaction prediction have been developed, and preliminary results have demonstrated their feasibility. Most of the existing domain-based methods, however, consider only single-domain pairs (one domain from one protein) and assume independence between domain-domain interactions.