ArticleNature methods2013
Interactome3D: adding structural details to protein networks.
Article in Nature methods, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 243 papers, 1 of them a synthesis that pooled it.
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Who cites it
243 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Alternative splicing fine-tunes modular protein interfaces to control protein localization.Nature structural & molecular biology · 2026Article
- PrePPI - Structure-based Prediction of Protein-protein Interactomes and Networks.Journal of molecular biology · 2026Article
- Variant characterization in the intrinsically disordered human proteome.Nature structural & molecular biology · 2026Article
- DirectContacts2: a wiring diagram of human physical protein interactions.Nature communications · 2026Article
- Network-driven discovery of repurposable drugs targeting hallmarks of aging.Nature aging · 2026Article
- The aging genome exhibits organized vulnerability to somatic mutations.bioRxiv : the preprint server for biology · 2026Article
- A tri-modal contrastive learning framework for protein representation learning.Cell reports methods · 2026Article
- Proteome-wide prediction of interactions between structured domains and peptide motifs reveals functionally coherent subnetworks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Targeting protein protein interactions and their modulators to enable new therapeutic strategies for human diseases.NPJ systems biology and applications · 2026Review
- Experimental assessment of AI-based interactome mapping.Nature communications · 2026Article
- Allostery in Biomolecular Condensates.Journal of molecular biology · 2026Review
- Effector-host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation.Nature microbiology · 2026Article
- Complex genetic landscape in CLL: Clinical impact on patients' survival and insights into the altered molecular pathways.Molecular therapy. Oncology · 2025Article
- Unraveling cooperative and competitive interactions within protein triplets in the human interactome.Scientific reports · 2025Article
- A structurally informed human protein-protein interactome reveals proteome-wide perturbations caused by disease mutations.Nature biotechnology · 2025Article
- Global profiling of protein complex dynamics with an experimental library of protein interaction markers.Nature biotechnology · 2025Article
- An AlphaFold guided model for the evolution of the CaMKII interactome.bioRxiv : the preprint server for biology · 2025Article
- Target Mapping in Cancer: Ligandable Protein Pockets on 3D OncoPPI Networks.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Causal association of cholesterol metabolism-related proteins with hepatocellular carcinoma and dysfunction-associated steatotic liver disease: a mendelian randomization study.Discover oncology · 2025Article
183 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Network-centered approaches are increasingly used to understand the fundamentals of biology. However, the molecular details contained in the interaction networks, often necessary to understand cellular processes, are very limited, and the experimental difficulties surrounding the determination of protein complex structures make computational modeling techniques paramount. Here we present Interactome3D, a resource for the structural annotation and modeling of protein-protein interactions. Through the integration of interaction data from the main pathway repositories, we provide structural details at atomic resolution for over 12,000 protein-protein interactions in eight model organisms. Unlike static databases, Interactome3D also allows biologists to upload newly discovered interactions and pathways in any species, select the best combination of structural templates and build three-dimensional models in a fully automated manner. Finally, we illustrate the value of Interactome3D through the structural annotation of the complement cascade pathway, rationalizing a potential common mechanism of action suggested for several disease-causing mutations.
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Registered trials
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.