ArticleMolecular cell2025
Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions.
Article in Molecular cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Avl9 defines a family of DENN domain GTPase-activating proteins.The Journal of cell biology · 2026Article
- N4BP1 uses tandem KH domains to associate with EDC4 and mRNA decapping factors in P-bodies.Communications biology · 2026Article
- Protein-protein interaction network architecture of human polygenic traits reveals domain-spanning connectivity and evolutionary pressures.Genome biology · 2026Article
- The predicted interactome of the human mitochondrial proteome.Nature communications · 2026Article
- Integrated Multi-omics Reveals CDKN1A Suppression and Metabolic Regulation as Key Mechanisms of Huangqi Guizhi Wuwu Decoction Against Doxorubicin-Induced Cardiotoxicity.Cardiovascular toxicology · 2026Article
- Deciphering protein mutation-phenotype linkages from CRISPR-based tiling mutagenesis screens.Cell systems · 2026Article
- RTF2 and CLASPIN localize CHK1 to the replication fork to control S-phase progression.Science advances · 2026Article
- A functional atlas of transposon-encoded products and their integration into host networks.Nature communications · 2026Article
- The penicillin-binding protein PBP1b fortifies the Escherichia coli division site against osmotic rupture.Nature microbiology · 2026Article
- Genome-wide association study identifies toll-like receptor four protein-mediated metabolic remodelling affecting gout pathogenesis.Journal of global health · 2026Observational
- Salmonella SopB suppresses post-transcriptionally regulated cytokine release to reduce early tissue inflammation and delay disease progression.Nature communications · 2026Article
- Article
- A broadly conserved gram-positive lipoprotein regulates cell elongation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A CHK1-mediated phosphorylation switch suppresses human Topoisomerase 1-associated genomic instability.The EMBO journal · 2026Article
- The SPARK complex forms the molecular basis of vertebrate fertilization.bioRxiv : the preprint server for biology · 2026Article
- A dating app for extracellular adhesion proteins.Cell genomics · 2026Article
- FlyPredictome: A structural atlas of predicted protein-protein interactions inbioRxiv : the preprint server for biology · 2026Article
- Structure and function of IWS1 in transcription elongation.Nucleic acids research · 2026Article
- Protein foundation models: a comprehensive survey.Science China. Life sciences · 2026Review
- LuxS/AI-2 regulates phoP/phoQ by a non-canonical mechanism to enhance acid stress survival in Salmonella Typhimurium.PLoS pathogens · 2026Article
3 more citing papers are in PubMed but not listed here.
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Abstract
Protein-protein interactions (PPIs) are ubiquitous in biology, yet a comprehensive structural characterization of the PPIs underlying cellular processes is lacking. AlphaFold-Multimer (AF-M) has the potential to fill this knowledge gap, but standard AF-M confidence metrics do not reliably separate relevant PPIs from an abundance of false positive predictions. To address this limitation, we used machine learning on curated datasets to train a structure prediction and omics-informed classifier (SPOC) that effectively separates true and false AF-M predictions of PPIs, including in proteome-wide screens. We applied SPOC to an all-by-all matrix of nearly 300 human genome maintenance proteins, generating ∼40,000 predictions that can be viewed at predictomes.org, where users can also score their own predictions with SPOC. High-confidence PPIs discovered using our approach enable hypothesis generation in genome maintenance. Our results provide a framework for interpreting large-scale AF-M screens and help lay the foundation for a proteome-wide structural interactome.
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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.