ReviewFrontiers in molecular biosciences2021
Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds.
Review in Frontiers in molecular biosciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 34 citations in OpenAlex.
- Universal and Lineage-Specific Patterns in the Distribution of ECOD Domain Homology Groups Across Superkingdoms.Proteins · 2026Article
- AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2.Nature methods · 2026Article
- Gene function predicts divergence across molecular levels.bioRxiv : the preprint server for biology · 2026Article
- Prebiotically Plausible Peptides can Self-assemble into β-rich Nanostructures.bioRxiv : the preprint server for biology · 2025Article
- Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.G3 (Bethesda, Md.) · 2025Article
- Exploring structural diversity across the protein universe with The Encyclopedia of Domains.Science (New York, N.Y.) · 2024Article
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- Clustering protein functional families at large scale with hierarchical approaches.Protein science : a publication of the Protein Society · 2024Article
- Peptides En Route from Prebiotic to Biotic Catalysis.Accounts of chemical research · 2024Article
- Protein superfolds are characterised as frustration-free topologies: A case study of pure parallel β-sheet topologies.PLoS computational biology · 2024Article
- Amino-Acid Characteristics in Protein Native State Structures.Biomolecules · 2024Article
- Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis.Journal of microbiology (Seoul, Korea) · 2024Review
- ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2.PLoS computational biology · 2024Article
- Article
- Alternative Reading Frames are an Underappreciated Source of Protein Sequence Novelty.Journal of molecular evolution · 2023Review
- Short Linear Motifs Orchestrate Functioning of Human Proteins during Embryonic Development, Redox Regulation, and Cancer.Metabolites · 2022Article
- Structure of putative tumor suppressor ALDH1L1.Communications biology · 2022Article
- 3D-Printed Protein Models as an Educational Tool in Biochemistry Outreach.Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular BiologyArticle
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This article is dedicated to the memory of Cyrus Chothia, who was a leading light in the world of protein structure evolution. His elegant analyses of protein families and their mechanisms of structural and functional evolution provided important evolutionary and biological insights and firmly established the value of structural perspectives. He was a mentor and supervisor to many other leading scientists who continued his quest to characterise structure and function space. He was also a generous and supportive colleague to those applying different approaches. In this article we review some of his accomplishments and the history of protein structure classifications, particularly SCOP and CATH. We also highlight some of the evolutionary insights these two classifications have brought. Finally, we discuss how the expansion and integration of protein sequence data into these structural families helps reveal the dark matter of function space and can inform the emergence of novel functions in Metazoa. Since we cover 25 years of structural classification, it has not been feasible to review all structure based evolutionary studies and hence we focus mainly on those undertaken by the SCOP and CATH groups and their collaborators.
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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.