ArticleeLife2014
Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.
Article in eLife, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 379 papers.
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Who cites it
379 citing papers in PubMed.
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- Structure and evolution-guided design of minimal RNA-guided nucleases.Science (New York, N.Y.) · 2026Article
- Linear-time prediction of proteome-scale microbial protein interactions.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Identification of 14-3-3 Proteins as Binding Partners of TRP Channels.Journal of chemical information and modeling · 2026Article
- Enhancing mutation impact prediction in protein-protein interactions through interpretable graph-based multi-level feature interactions.Bioinformatics (Oxford, England) · 2026Article
- Influenza hemagglutinin subtypes have different sequence constraints despite sharing extremely similar structures.bioRxiv : the preprint server for biology · 2026Article
- Engineered kin recognition specificities in the TraA cell surface receptor.The ISME journal · 2026Article
- Stepwise DNA unwinding gates TnpB genome-editing activity.bioRxiv : the preprint server for biology · 2026Article
- Influenza hemagglutinin subtypes have different sequence constraints despite sharing extremely similar structures.Virus evolution · 2026Article
- Predicting Protein-Protein Interactions from Machine-Learned Representations.Advances in experimental medicine and biology · 2026Review
- Cryo-EM structures of plant Augmin reveal coiled-coil assembly, antiparallel dimerization, and NEDD1 binding.Nature communications · 2025Article
- Structure and evolution-guided design of minimal RNA-guided nucleases.bioRxiv : the preprint server for biology · 2025Article
- Protein design drives synthetic biology research of plant natural products.Biodesign research · 2025Review
- A genomic perspective on fungal diversity and evolution.Nature reviews. Microbiology · 2025Review
- An AlphaFold guided model for the evolution of the CaMKII interactome.bioRxiv : the preprint server for biology · 2025Article
- Review
- Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Message hidden in α-helices-toward a better understanding of plant ABCG transporters' multispecificity.Plant physiology · 2025Article
319 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. We find that residue pairs identified using a pseudo-likelihood-based method to covary across protein-protein interfaces in the 50S ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex, provided that the number of aligned sequences is greater than the average length of the two proteins. We use this method to make subunit contact predictions for an additional 36 protein complexes with unknown structures, and present models based on these predictions for the tripartite ATP-independent periplasmic (TRAP) transporter, the tripartite efflux system, the pyruvate formate lyase-activating enzyme complex, and the methionine ABC transporter.DOI: http://dx.doi.org/10.7554/eLife.02030.001.
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Registered trials
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