Nucleic Acids Research · 2010 · 189 citations · 22 references
EngineeringMolecular BiologyDomain InteractionsUpdated DomineDomain CharacteristicData ScienceManagementData IntegrationProteomicsBiochemistryInteractomicsPredictive AnalyticsKnowledge DiscoveryProtein ModelingOmicsPathway AnalysisComputer ScienceProtein Structure PredictionBioinformaticsFunctional GenomicsProtein BioinformaticsDomain AdaptationComputational BiologySystems BiologyUnique DdisDomain ModelDomain-specific ModelingDomain-domain InteractionsData Modeling
DOMINE aggregates known and predicted domain‑domain interactions from 15 sources. DOMINE is intended as a reference for researchers studying protein and domain interactions, aiding both bench scientists and bioinformaticians in testing and predicting novel protein–protein interactions. The updated DOMINE now contains 26,219 unique DDIs—an increase of 23%—including 6,634 known interactions, 2,285 structure‑derived DDIs, and about 3,500 computational predictions, and introduces a confidence‑level classification for predicted DDIs. The database is accessible at http://domine.utdallas.edu.
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.
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Inferring Domain–Domain Interactions From Protein–Protein Interactions
Minghua Deng, Shipra Mehta, Fengzhu Sun et al. · Genome Research · 2002 · 447 citations · Full text
Prediction of protein–protein interactions using random decision forest framework
Xuewen Chen, Mei Liu · Bioinformatics · 2005 · 386 citations · Full text