DAPID is a database of domain-annotated protein interactions inferred from 
three-dimensional (3D) interacting domains of protein complexes in the Protein 
Data Bank (PDB). The DAPID data model allows users to visualize 3D interacting 
domains, contact residues, and molecular details of any predicted 
protein-protein interactions. Our model derives these interactions by utilizing 
a new concept, called the ''3D-domain interologs'' which is similar to 
''interologs''. In S. cerevisiae, there is 18.6% overlap between our predicted 
protein-protein interactions and ones in the DIP database. The mean correlation 
coefficient of the gene expression profiles of our predicted interactions is 
significantly higher than that for random pairs in S. cerevisiae. In addition, 
we find several novel interactions which are consistent with the functions of 
the proteins. The DAPID currently holds 1008 3D-interacting domain pairs and 
101511 predicted 3D-domain annotated protein-protein interactions. It is 
available online at http://gemdock.life.nctu.edu.tw/dapid.