ArticleNucleic acids research2011
DOMINE: a comprehensive collection of known and predicted domain-domain interactions.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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Who cites it
90 citing papers in PubMed.
- Predicting functions of uncharacterized gene products from microbial communities.Nature biotechnology · 2026Article
- Splitpea: a Python package for protein-protein interaction network rewiring analysis due to alternative splicing.Bioinformatics (Oxford, England) · 2026Article
- ProteoformDB: an integrative database for functional roles of proteoforms.Database : the journal of biological databases and curation · 2026Article
- PPI-ID: Streamlining protein-protein interaction prediction through domain and SLiM mapping.PLoS computational biology · 2025Article
- DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders.Nucleic acids research · 2025Article
- Computational insights into host-pathogen protein interactions: unveiling penaeid shrimp and white spot syndrome virus interplay.Molecular genetics and genomics : MGG · 2025Article
- PPIXpress and PPICompare webservers infer condition-specific and differential PPI networks.Bioinformatics advances · 2025Article
- Integration of molecular coarse-grained model into geometric representation learning framework for protein-protein complex property prediction.Nature communications · 2024Article
- Integrating multi-omics to unravel host-microbiome interactions in inflammatory bowel disease.Cell reports. Medicine · 2024Review
- Generation of a high confidence set of domain-domain interface types to guide protein complex structure predictions by AlphaFold.Bioinformatics (Oxford, England) · 2024Article
- HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes.Genomics, proteomics & bioinformatics · 2023Article
- Analysis of Host-Bacteria Protein Interactions Reveals Conserved Domains and Motifs That Mediate Fundamental Infection Pathways.International journal of molecular sciences · 2022Article
- PFP-GO: Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms.Frontiers in genetics · 2022Article
- Annotated protein network analysis linking oral diseases.Bioinformation · 2022Article
- Computational prediction and experimental validation ofFrontiers in cellular and infection microbiology · 2022Article
- Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection.Methods in molecular biology (Clifton, N.J.) · 2022Article
- HMGA1 stimulates MYH9-dependent ubiquitination of GSK-3β via PI3K/Akt/c-Jun signaling to promote malignant progression and chemoresistance in gliomas.Cell death & disease · 2021Article
- Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases.Genome biology · 2021Article
- PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.PLoS computational biology · 2021Article
- Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data.Frontiers in bioinformatics · 2021Review
30 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
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.
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