Inferring protein domain interactions from databases of interacting proteins

We describe domain pair exclusion analysis ( DPEA), a method for inferring domain interactions from databases of interacting proteins. DPEA features a log odds score, E-ij, reflecting confidence that domains i and j interact. We analyzed 177,233 potential domain interactions underlying 26,032 protein interactions. In total, 3,005 high-confidence domain interactions were inferred, and were evaluated using known domain interactions in the Protein Data Bank. DPEA may prove useful in guiding experiment-based discovery of previously unrecognized domain interactions.