ArticleProceedings of the National Academy of Sciences of the United States of America2016
Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
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- Allostery is a widespread cause of loss-of-function variant pathogenicity.Nature communications · 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
- Accurate protein-protein interactions modeling through physics-informed geometric invariant learning.Communications biology · 2026Article
- Computational design of class II MHC binding peptide with sequence-based evolution information.Bioinformatics advances · 2026Article
- Cryo-EM structures of plant Augmin reveal coiled-coil assembly, antiparallel dimerization, and NEDD1 binding.Nature communications · 2025Article
- High-accuracy protein complex structure modeling based on sequence-derived structure complementarity.Nature communications · 2025Article
- Direct coupling analysis and the attention mechanism.BMC bioinformatics · 2025Article
- DiffPaSS-high-performance differentiable pairing of protein sequences using soft scores.Bioinformatics (Oxford, England) · 2024Article
- The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction.Biomolecules · 2024Review
- Impact of phylogeny on the inference of functional sectors from protein sequence data.PLoS computational biology · 2024Article
- Pairing interacting protein sequences using masked language modeling.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies.Biophysical journal · 2024Article
- Enhancing coevolutionary signals in protein-protein interaction prediction through clade-wise alignment integration.Scientific reports · 2024Article
- Generating interacting protein sequences using domain-to-domain translation.Bioinformatics (Oxford, England) · 2023Article
- Latent generative landscapes as maps of functional diversity in protein sequence space.Nature communications · 2023Article
- Undersampling and the inference of coevolution in proteins.Cell systems · 2023Article
- Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins.PLoS computational biology · 2023Article
- Analysis of CheW-like domains provides insights into organization of prokaryotic chemotaxis systems.Proteins · 2023Article
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Authors and funding
5 authors.
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Abstract
Understanding protein-protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein-protein interactions are urgently needed. Such methods should connect multiple scales from evolutionary conserved interactions between families of homologous proteins, over the identification of specifically interacting proteins in the case of multiple paralogs inside a species, down to the prediction of residues being in physical contact across interaction interfaces. Statistical inference methods detecting residue-residue coevolution have recently triggered considerable progress in using sequence data for quaternary protein structure prediction; they require, however, large joint alignments of homologous protein pairs known to interact. The generation of such alignments is a complex computational task on its own; application of coevolutionary modeling has, in turn, been restricted to proteins without paralogs, or to bacterial systems with the corresponding coding genes being colocalized in operons. Here we show that the direct coupling analysis of residue coevolution can be extended to connect the different scales, and simultaneously to match interacting paralogs, to identify interprotein residue-residue contacts and to discriminate interacting from noninteracting families in a multiprotein system. Our results extend the potential applications of coevolutionary analysis far beyond cases treatable so far.
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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.