3did: a catalogue of domain-based interactions of known three-dimensional structure

The database of three-dimensional (3D) interacting domains (3did, available online for browsing and bulk download at http://3did.irbbarcelona.org) is a catalogue of protein-protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural templates of domain-domain interactions in the Protein Data Bank, providing molecular details for such interactions. The current version also includes a pipeline for the discovery and annotation of novel domain-motif interactions. For every interaction, 3did identifies and groups different binding modes by clustering similar interfaces into “interaction topologies”. By maintaining a constantly updated collection of domain-based structural interaction templates, 3did is a reference source of information for the structural characterization of protein interaction networks. 3did is updated every six months.