ArticleJournal of molecular biology2020
Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design.
Article in Journal of molecular biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- TEDLH: domain HMMs for sensitive detection of remote homologues.Bioinformatics (Oxford, England) · 2026Article
- Stability and cooperativity in chimeric de novo TIM barrels via quarter swapping.Protein science : a publication of the Protein Society · 2026Article
- Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes.Proteins · 2025Article
- On the emergence of metabolism: the evolution of proteins that powered life.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record.Genome biology and evolution · 2025Article
- Addressing epistasis in the design of protein function.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Engineering strategies and challenges of endolysin as an antibacterial agent against Gram-negative bacteria.Microbial biotechnology · 2024Review
- Retracing the evolution of a modern periplasmic binding protein.Protein science : a publication of the Protein Society · 2023Article
- Protein salvage and repurposing in evolution: Phospholipase D toxins are stabilized by a remodeled scrap of a membrane association domain.Protein science : a publication of the Protein Society · 2023Article
- Creative destruction: New protein folds from old.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Insertions and deletions mediated functional divergence of Rossmann fold enzymes.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- ProtGPT2 is a deep unsupervised language model for protein design.Nature communications · 2022Article
- Mechanisms of protein evolution.Protein science : a publication of the Protein Society · 2022Review
- Evidence for the emergence of β-trefoils by 'Peptide Budding' from an IgG-like β-sandwich.PLoS computational biology · 2022Article
- Folding and Evolution of a Repeat Protein on the Ribosome.Frontiers in molecular biosciences · 2022Article
- Structural dynamics in the evolution of a bilobed protein scaffold.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- ProteinTools: a toolkit to analyze protein structures.Nucleic acids research · 2021Article
- Evolution, folding, and design of TIM barrels and related proteins.Current opinion in structural biology · 2021Review
- Bridging Themes: Short Protein Segments Found in Different Architectures.Molecular biology and evolution · 2021Article
- Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks.Frontiers in molecular biosciences · 2021Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Natural evolution has generated an impressively diverse protein universe via duplication and recombination from a set of protein fragments that served as building blocks. The application of these concepts to the design of new proteins using subdomain-sized fragments from different folds has proven to be experimentally successful. To better understand how evolution has shaped our protein universe, we performed an all-against-all comparison of protein domains representing all naturally existing folds and identified conserved homologous protein fragments. Overall, we found more than 1000 protein fragments of various lengths among different folds through similarity network analysis. These fragments are present in very different protein environments and represent versatile building blocks for protein design. These data are available in our web server called F(old P)uzzle (fuzzle.uni-bayreuth.de), which allows to individually filter the dataset and create customized networks for folds of interest. We believe that our results serve as an invaluable resource for structural and evolutionary biologists and as raw material for the design of custom-made proteins.
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