ArticleNature structural & molecular biology2023
Hallucination of closed repeat proteins containing central pockets.
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 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 12 citations in OpenAlex.
- Accelerating protein design by scaling experimental characterization.Nature communications · 2026Article
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- De novo protein design: a transformative frontier in clinical protein applications.Journal of translational medicine · 2026Review
- Design of Orthogonal Far-Red, Orange and Green Fluorophore-binding Proteins for Multiplex Imaging.bioRxiv : the preprint server for biology · 2025Article
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- Article
- Utilizing AfDesign for Developing a Small Molecule Inhibitor of PICK- 1-PDZ.Current protein & peptide science · 2025Article
- De novo design and evolution of an artificial metathase for cytoplasmic olefin metathesis.Nature catalysis · 2025Article
- Binding and sensing diverse small molecules using shape-complementary pseudocycles.Science (New York, N.Y.) · 2024Article
- Protein Design Using Structure-Prediction Networks: AlphaFold and RoseTTAFold as Protein Structure Foundation Models.Cold Spring Harbor perspectives in biology · 2024Review
- De novo design of alpha-beta repeat proteins.bioRxiv : the preprint server for biology · 2024Article
- De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles.bioRxiv : the preprint server for biology · 2023Article
- Intelligent Protein Design and Molecular Characterization Techniques: A Comprehensive Review.Molecules (Basel, Switzerland) · 2023Review
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
Abstract
In pseudocyclic proteins, such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern, giving rise to a central cavity that can serve as a pocket for ligand binding or enzymatic activity. Inspired by these proteins, we devised a deep-learning-based approach to broadly exploring the space of closed repeat proteins starting from only a specification of the repeat number and length. Biophysical data for 38 structurally diverse pseudocyclic designs produced in Escherichia coli are consistent with the design models, and the three crystal structures we were able to obtain are very close to the designed structures. Docking studies suggest the diversity of folds and central pockets provide effective starting points for designing small-molecule binders and enzymes.
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What OpenQuestion holds
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.