ArticleThe Journal of biological chemistry2012
Use of structural phylogenetic networks for classification of the ferritin-like superfamily.
Article in The Journal of biological chemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- A structure-aware generative AI framework for revealing functional relationships in protein families.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Iron and peroxide regulation of the PrrF sRNAs and a conserved ferritin family protein inJournal of bacteriology · 2026Article
- Mini-bacterioferritins: structural insight into a ferritin-like protein from the anaerobic methane-oxidising archaeon Candidatus Methanoperedens carboxydivorans.Communications biology · 2026Article
- Structural, functional, and evolutionary perspectives of bacterial iron repertoire: bacterioferritin and bacterioferritin-associated ferredoxin as emerging targets against antibiotic resistance.Folia microbiologica · 2026Review
- Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments.Genome biology and evolution · 2026Article
- MD-Phylogeny: Constructing Statistically Supported Phylogenetic Trees from Protein Structures Using Molecular Dynamics.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Studying the Evolution of Protein Structure One Superfamily at a Time.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A Pipeline for Generating Datasets of Three-Dimensional Tertiary Interaction Characters for Model-Based Structural Phylogenetics.Methods in molecular biology (Clifton, N.J.) · 2026Article
- An Introduction to Structural Phylogenetics for Biomedical Sciences.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The Mechanism of Mineral Nucleation and Growth in a Mini-Ferritin.Journal of the American Chemical Society · 2025Article
- A fast approach for structural and evolutionary analysis based on energetic profile protein comparison.Nature communications · 2025Article
- Structural and Evolutionary Analysis of Proteins Endowed with a Nucleotidyltransferase, or Non-canonical Palm, Catalytic Domain.Journal of molecular evolution · 2024Article
- Metabolite phosphatase from anhydrobiotic tardigrades.The FEBS journal · 2024Article
- Structural Phylogenetics with Protein Mass Spectrometry: A Proof-of-Concept.The protein journal · 2024Article
- The crystal structure of Acinetobacter baumannii bacterioferritin reveals a heteropolymer of bacterioferritin and ferritin subunits.Scientific reports · 2024Article
- Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships.bioRxiv : the preprint server for biology · 2024Article
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- Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships.Virus evolution · 2024Article
- A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the postgenomic era, bioinformatic analysis of sequence similarity is an immensely powerful tool to gain insight into evolution and protein function. Over long evolutionary distances, however, sequence-based methods fail as the similarities become too low for phylogenetic analysis. Macromolecular structure generally appears better conserved than sequence, but clear models for how structure evolves over time are lacking. The exponential growth of three-dimensional structural information may allow novel structure-based methods to drastically extend the evolutionary time scales amenable to phylogenetics and functional classification of proteins. To this end, we analyzed 80 structures from the functionally diverse ferritin-like superfamily. Using evolutionary networks, we demonstrate that structural comparisons can delineate and discover groups of proteins beyond the "twilight zone" where sequence similarity does not allow evolutionary analysis, suggesting that considerable and useful evolutionary signal is preserved in three-dimensional structures.
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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.