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
ˇ§3D-domain interologsˇ¨
which is similar to ˇ§interologsˇ¨. The 3D-domain interologs,
the core idea of our DAPID method, is defined as
"Domain a (in chain A) interacts with domain b (in chain B) in a known 3D complex,
their inferring protein pair A' (containing domain a ) and B' (containing domain b )
in the same species would be likely to interact with each other
if both protein pairs (A' and A as well as proteins B and B') are homologous".
In S. cerevisiae, there is 18.6% overlap between
our predicted protein-protein interactions and 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 includes
1008 3D-interacting domain pairs and
101511 predicted 3D-domain annotated protein-protein interactions.
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