ArticleNature methods2009
An experimentally derived confidence score for binary protein-protein interactions.
Article in Nature methods, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 245 papers.
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Who cites it
245 citing papers in PubMed.
- Variant characterization in the intrinsically disordered human proteome.Nature structural & molecular biology · 2026Article
- FlyPredictome: A structural atlas of predicted protein-protein interactions inbioRxiv : the preprint server for biology · 2026Article
- NeuroViOme: a viral orfeome collection for studies of neurodegenerative disease.Journal of neurovirology · 2026Review
- Quantum-augmented graph differential geometry enhances accuracy in protein-protein interaction prediction.Scientific reports · 2026Article
- Interactomics: Dissecting Protein Networks in Living Systems.Advances in experimental medicine and biology · 2026Review
- A Structure-Guided Kinase-Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome.bioRxiv : the preprint server for biology · 2025Article
- The Constrained Disorder Principle: A Paradigm Shift for Accurate Interactome Mapping and Information Analysis in Complex Biological Systems.Bioengineering (Basel, Switzerland) · 2025Review
- Bacterial two-hybrid systems evolved: innovations for protein-protein interaction research.Journal of bacteriology · 2025Review
- ProtLoc-GRPO: Cell line-specific subcellular localization prediction using a graph-based model and reinforcement learning.bioRxiv : the preprint server for biology · 2025Article
- PorV factor of the type IX secretion system and PosF porin act as adhesins in Riemerella anatipestifer infection.Veterinary research · 2025Article
- Evaluating sequence and structural similarity metrics for predicting shared paralog functions.NAR genomics and bioinformatics · 2025Article
- Transcription factors form a ternary complex with NIPBL/MAU2 to localize cohesin at enhancers.Nucleic acids research · 2025Article
- FlyPhoneDB2: A computational framework for analyzing cell-cell communication inComputational and structural biotechnology journal · 2025Article
- Host-pathogen protein interaction studies: quality control of cDNA libraries using nanopore sequencing.PloS one · 2025Article
- High-Throughput Yeast Two-Hybrid Technology for Investigating Molecular Virology.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A comprehensive two-hybrid analysis to explore themSystems · 2024Article
- Accurate and sensitive interactome profiling using a quantitative protein-fragment complementation assay.Cell reports methods · 2024Article
- Cell surface protein-protein interaction profiling for biological network analysis and novel target discovery.Life medicine · 2024Review
- WeSA: a web server for improving analysis of affinity proteomics data.Nucleic acids research · 2024Article
- Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells.Nature biomedical engineering · 2024Article
185 more citing papers are in PubMed but not listed here.
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Authors and funding
20 authors.
Funding
Abstract
Information on protein-protein interactions is of central importance for many areas of biomedical research. At present no method exists to systematically and experimentally assess the quality of individual interactions reported in interaction mapping experiments. To provide a standardized confidence-scoring method that can be applied to tens of thousands of protein interactions, we have developed an interaction tool kit consisting of four complementary, high-throughput protein interaction assays. We benchmarked these assays against positive and random reference sets consisting of well documented pairs of interacting human proteins and randomly chosen protein pairs, respectively. A logistic regression model was trained using the data from these reference sets to combine the assay outputs and calculate the probability that any newly identified interaction pair is a true biophysical interaction once it has been tested in the tool kit. This general approach will allow a systematic and empirical assignment of confidence scores to all individual protein-protein interactions in interactome networks.
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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.