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Inferring protein domain interactions from databases of interacting proteins

Robert Riley1, Christopher Lee2, Chiara Sabatti1 and David Eisenberg23*

Author Affiliations

1 Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA 90095, USA

2 Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA

3 Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095-1570, USA

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Genome Biology 2005, 6:R89  doi:10.1186/gb-2005-6-10-r89

Published: 19 September 2005

Abstract

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.