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Genome Biol. 2005;6(10):R89. Epub 2005 Sep 19.

Inferring protein domain interactions from databases of interacting proteins.

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  • 1Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, CA 90095, USA. riley@mbi.ucla.edu


We describe domain pair exclusion analysis (DPEA), a method for inferring domain interactions from databases of interacting proteins. DPEA features a log odds score, Eij, 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.

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