Inferring protein domain interactions from databases of interacting proteins
Open Access
- 19 September 2005
- journal article
- research article
- Published by Springer Nature in Genome Biology
- Vol. 6 (10) , R89
- https://doi.org/10.1186/gb-2005-6-10-r89
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, 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.Keywords
This publication has 47 references indexed in Scilit:
- Novel specificities emerge by stepwise duplication of functional modulesGenome Research, 2005
- Genomic analysis of essentiality within protein networksPublished by Elsevier ,2004
- A Protein Interaction Map of Drosophila melanogasterScience, 2003
- The gelsolin family of actin regulatory proteins: modular structures, versatile functionsPublished by Wiley ,2003
- Assembly of Cell Regulatory Systems Through Protein Interaction DomainsScience, 2003
- Functional organization of the yeast proteome by systematic analysis of protein complexesNature, 2002
- Protein function in the post-genomic eraNature, 2000
- A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiaeNature, 2000
- From Src Homology domains to other signaling modules: proposal of the `protein recognition code'Oncogene, 1998
- Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domainsNature, 1994