ArticleNature structural & molecular biology2023
Exploration of novel αβ-protein folds through de novo design.
Article in Nature structural & molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Distinct energetic blueprints diversify function of conserved protein folds.Nature chemistry · 2026Article
- RINAMI: Residue-attributed interpretable neural network for predicting absolute folding free energy by merging structure and sequence information.Protein science : a publication of the Protein Society · 2026Article
- Tangled Tail of Mechanically Interlocked Peptides.Journal of the American Chemical Society · 2026Review
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- Limitations of the refolding pipeline for de novo protein design.Protein science : a publication of the Protein Society · 2026Article
- Negative design enables cell-free expression and folding of designed transmembrane β-barrels.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Evaluating zero-shot prediction of monomeric protein design success by AlphaFold, ESMFold, and ProteinMPNN.Protein science : a publication of the Protein Society · 2026Article
- Protein engineering: status report.Protein engineering, design & selection : PEDS · 2026Review
- Rapid discovery of new-to-nature protein domains by novelty-first forcing of language models.bioRxiv : the preprint server for biology · 2025Article
- The Role of AI-Driven De Novo Protein Design in the Exploration of the Protein Functional Universe.Biology · 2025Review
- Scalable protein design using optimization in a relaxed sequence space.Science (New York, N.Y.) · 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
- Diversifying de novo TIM barrels by hallucination.Protein science : a publication of the Protein Society · 2024Article
- Sparks of function by de novo protein design.Nature biotechnology · 2024Review
- Article
- In silico protein dynamics in the human cytoplasm: Partial folding, misfolding, fold switching, and non-native interactions.Protein science : a publication of the Protein Society · 2023Article
- The Structural Rule Distinguishing a Superfold: A Case Study of Ferredoxin Fold and the Reverse Ferredoxin Fold.Molecules (Basel, Switzerland) · 2022Article
- Identifying well-foldedFrontiers in molecular biosciences · 2022Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A fundamental question in protein evolution is whether nature has exhaustively sampled nearly all possible protein folds throughout evolution, or whether a large fraction of the possible folds remains unexplored. To address this question, we defined a set of rules for β-sheet topology to predict novel αβ-folds and carried out a systematic de novo protein design exploration of the novel αβ-folds predicted by the rules. The designs for all eight of the predicted novel αβ-folds with a four-stranded β-sheet, including a knot-forming one, folded into structures close to the design models. Further, the rules predicted more than 10,000 novel αβ-folds with five- to eight-stranded β-sheets; this number far exceeds the number of αβ-folds observed in nature so far. This result suggests that a vast number of αβ-folds are possible, but have not emerged or have become extinct due to evolutionary bias.
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