DOMINE: a comprehensive collection of known and predicted domain-domain interactions
Open Access
- 27 November 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 39 (suppl_1), D730-D735
- https://doi.org/10.1093/nar/gkq1229
Abstract
DOMINE is a comprehensive collection of known and predicted domain–domain interactions (DDIs) compiled from 15 different sources. The updated DOMINE includes 2285 new domain–domain interactions (DDIs) inferred from experimentally characterized high-resolution three-dimensional structures, and about 3500 novel predictions by five computational approaches published over the last 3 years. These additions bring the total number of unique DDIs in the updated version to 26 219 among 5140 unique Pfam domains, a 23% increase compared to 20 513 unique DDIs among 4346 unique domains in the previous version. The updated version now contains 6634 known DDIs, and features a new classification scheme to assign confidence levels to predicted DDIs. DOMINE will serve as a valuable resource to those studying protein and domain interactions. Most importantly, DOMINE will not only serve as an excellent reference to bench scientists testing for new interactions but also to bioinformaticans seeking to predict novel protein–protein interactions based on the DDIs. The contents of the DOMINE are available at http://domine.utdallas.edu .Keywords
This publication has 23 references indexed in Scilit:
- A discriminative approach for identifying domain–domain interactions from protein–protein interactionsProteins-Structure Function and Bioinformatics, 2009
- Knowledge-guided inference of domain–domain interactions from incomplete protein–protein interaction networksBioinformatics, 2009
- 3did Update: domain-domain and peptide-mediated interactions of known 3D structureNucleic Acids Research, 2008
- Interrogating domain-domain interactions with parsimony based approachesBMC Bioinformatics, 2008
- InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scaleGenome Biology, 2007
- Integrative approach for computationally inferring protein domain interactionsBioinformatics, 2003
- Assembly of Cell Regulatory Systems Through Protein Interaction DomainsScience, 2003
- Inferring Domain–Domain Interactions From Protein–Protein InteractionsGenome Research, 2002
- Correlated sequence-signatures as markers of protein-protein interactionJournal of Molecular Biology, 2001
- Domain combinations in archaeal, eubacterial and eukaryotic proteomesJournal of Molecular Biology, 2001