ArticleNature communications2021
Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
63 citing papers in PubMed, 131 citations in OpenAlex.
- xBind: an integrated webserver for large language model-enabled cross-molecular protein binding site prediction.Nucleic acids research · 2026Article
- Mechanosensing at the endoplasmic reticulum by IRE1.Research square · 2026Article
- ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein-protein interactions and gene essentiality across taxa.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Mechanistic basis of teichoic acid transport by a gatekeeper flippase.Nature communications · 2026Article
- Limited directional selection but coevolutionary signals among imprinted genes inbioRxiv : the preprint server for biology · 2026Article
- Conformations and sequence determinants in the lipid binding of an adhesive peptide derived from Vibrio cholerae biofilms.PLoS pathogens · 2026Article
- Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats.Antibiotics (Basel, Switzerland) · 2026Article
- Co-Var, a Measure to Determine Intra-protein, Inter-protein, Protein-DNA, or Protein-RNA Coevolution.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Ultraweak interactions drive cap-mediated positioning and elongation of the bacterial flagellar filament.Nature communications · 2025Article
- Towards a phylogenetically informed approach to solving protein-protein interactions.Biochemical Society transactions · 2025Review
- AbAgym: a well-curated dataset for the mutational analysis of antibody-antigen complexes.mAbs · 2025Article
- Training bias and sequence alignments shape protein-peptide docking by AlphaFold and related methods.Protein science : a publication of the Protein Society · 2025Article
- Proteins need extra attention: improving the predictive power of protein language models on mutational datasets with hint tokens.NAR genomics and bioinformatics · 2025Article
- The structure of the complete extracellular bacterial flagellum reveals the mechanism of flagellin incorporation.Nature microbiology · 2025Article
- LncRNA-Protein Interactions: A Key to Deciphering LncRNA Mechanisms.Biomolecules · 2025Review
- Recent progress and future challenges in structure-based protein-protein interaction prediction.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold2.Research square · 2025Article
- Dual functional POGases from bacteria encompassing broader O-glycanase and adhesin activities.Nature communications · 2025Article
- Robust genome and cell engineering via in vitro and in situ circularized RNAs.Nature biomedical engineering · 2025Article
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Increasing numbers of protein interactions have been identified in high-throughput experiments, but only a small proportion have solved structures. Recently, sequence coevolution-based approaches have led to a breakthrough in predicting monomer protein structures and protein interaction interfaces. Here, we address the challenges of large-scale interaction prediction at residue resolution with a fast alignment concatenation method and a probabilistic score for the interaction of residues. Importantly, this method (EVcomplex2) is able to assess the likelihood of a protein interaction, as we show here applied to large-scale experimental datasets where the pairwise interactions are unknown. We predict 504 interactions de novo in the E. coli membrane proteome, including 243 that are newly discovered. While EVcomplex2 does not require available structures, coevolving residue pairs can be used to produce structural models of protein interactions, as done here for membrane complexes including the Flagellar Hook-Filament Junction and the Tol/Pal complex.
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What OpenQuestion holds
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.