ArticleComputational and structural biotechnology journal2021
Leri: A web-server for identifying protein functional networks from evolutionary couplings.
Article in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 18 citations in OpenAlex.
- Molecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks.Molecular biotechnology · 2026Article
- Intramolecular competition generates pulsatory protein activity shaped by light, temperature, and evolution.bioRxiv : the preprint server for biology · 2025Article
- Genetic diversity and molecular evolution of 3-carboxymuconate cyclase (Gp60-70), the major antigen in pathogenicMycology · 2025Article
- Accurate prediction of protein function using statistics-informed graph networks.Nature communications · 2024Article
- Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes.Computational and structural biotechnology journal · 2021Article
- Improvement of the Stability and Activity of an LPMO Through Rational Disulfide Bonds Design.Frontiers in bioengineering and biotechnology · 2021Article
- Csf1: A Putative Lipid Transport Protein Required for Homeoviscous Adaptation of the Lipidome.Contact (Thousand Oaks (Ventura County, Calif.))Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Information on the co-evolution of amino acid pairs in a protein can be used for endeavors such as protein engineering, mutation design, and structure prediction. Here we report a method that captures significant determinants of proteins using estimated co-evolution information to identify networks of residues, termed "residue communities", relevant to protein function. On the benchmark dataset (67 proteins with both catalytic and allosteric residues), the Pearson's correlation between the identified residues in the communities at functional sites is 0.53, and it is higher than 0.8 by taking account of conserved residues derived from the method. On the endoplasmic reticulum-mitochondria encounter structure complex, the results indicate three distinguishable residue communities that are relevant to functional roles in the protein family, suggesting that the residue communities could be general evolutionary signatures in proteins. Based on the method, we provide a webserver for the scientific community to explore the signatures in protein families, which establishes a powerful tool to analyze residue-level profiling for the discovery of functional sites and biological pathway identification. This web-server is freely available for non-commercial users at https://kornmann.bioch.ox.ac.uk/leri/services/ecs.html, neither login nor e-mail required.
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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.