ArticleNucleic acids research2014
3did: a catalog of domain-based interactions of known three-dimensional structure.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 151 papers.
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Who cites it
151 citing papers in PubMed.
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- PDBe PISA: Enhanced Analysis of Macromolecular Interactions.Current protocols · 2026Article
- SpliceImpactR maps alternative RNA processing events driving protein functional diversity.Nucleic acids research · 2026Article
- Variant characterization in the intrinsically disordered human proteome.Nature structural & molecular biology · 2026Article
- Protein Self-Interaction in Cellular Function and Network Evolution: Molecular Mechanisms, AI-Driven Insights, and Therapeutic Potentials.International journal of molecular sciences · 2026Review
- Mapping of Phenotype Specific Host-Microbiome Protein-Protein Interaction Networks in Colorectal Cancer Using Deep Learning.International journal of molecular sciences · 2026Article
- DNAM-1 mediates NK-cell activation and host-pathogen interaction via direct binding to fungal cell wall proteases.Communications biology · 2026Article
- Splitpea: a Python package for protein-protein interaction network rewiring analysis due to alternative splicing.Bioinformatics (Oxford, England) · 2026Article
- Experimental assessment of AI-based interactome mapping.Nature communications · 2026Article
- DeepISO: deep learning-powered prediction of protein-protein interaction rewiring generated by alternative splicing.Genome biology · 2026Article
- DSS-PPI: a self-supervised graph learning framework for protein-protein interaction prediction via multimodal sequence semantics.BMC genomics · 2026Article
- Effector-host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation.Nature microbiology · 2026Article
- Pangenome-based network analysis of Acinetobacter baumannii reveals the landscape of conserved therapeutic targets.Molecular diversity · 2026Article
- ProteoformDB: an integrative database for functional roles of proteoforms.Database : the journal of biological databases and curation · 2026Article
- An Integrated Computational Method for Investigation of Structural and Functional Impacts of Host-Pathogen Interaction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A guide to building the matrisome interactome: from computational predictions to experimental validation.The FEBS journal · 2026Review
- Definition and Discovery of Tandem SH3-Binding Motifs Interacting with Members of the p47Biomolecules · 2025Article
- Relational subgraphs fused with complete subgraphs based on the knowledge graph for mining protein complexes.Scientific reports · 2025Article
- PPI-ID: Streamlining protein-protein interaction prediction through domain and SLiM mapping.PLoS computational biology · 2025Article
91 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The database of 3D interacting domains (3did, available online for browsing and bulk download at http://3did.irbbarcelona.org) is a catalog of protein-protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural templates of domain-domain interactions in the Protein Data Bank, providing molecular details for such interactions. The current version also includes a pipeline for the discovery and annotation of novel domain-motif interactions. For every interaction, 3did identifies and groups different binding modes by clustering similar interfaces into 'interaction topologies'. By maintaining a constantly updated collection of domain-based structural interaction templates, 3did is a reference source of information for the structural characterization of protein interaction networks. 3did is updated every 6 months.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.