ArticleNature structural & molecular biology2018
De novo design of a non-local β-sheet protein with high stability and accuracy.
Article in Nature structural & molecular biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 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
66 citing papers in PubMed, 131 citations in OpenAlex.
- 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
- 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
- De novo protein design: a transformative frontier in clinical protein applications.Journal of translational medicine · 2026Review
- Evaluating zero-shot prediction of monomeric protein design success by AlphaFold, ESMFold, and ProteinMPNN.Protein science : a publication of the Protein Society · 2026Article
- Protein folding stability estimation with explicit consideration of unfolded states.Nature communications · 2026Article
- Protein engineering: status report.Protein engineering, design & selection : PEDS · 2026Review
- Designing novel solenoid proteins with in silico evolution.Communications chemistry · 2025Article
- Article
- Parametrically guided design of beta barrels and transmembrane nanopores using deep learning.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A self-assembled protein β-helix as a self-contained biofunctional motif.Nature communications · 2025Article
- AI Prediction of Structural Stability of Nanoproteins Based on Structures and Residue Properties by Mean Pooled Dual Graph Convolutional Network.Interdisciplinary sciences, computational life sciences · 2025Article
- Parametrically guided design of beta barrels and transmembrane nanopores using deep learning.bioRxiv : the preprint server for biology · 2025Article
- Opportunities and challenges in design and optimization of protein function.Nature reviews. Molecular cell biology · 2024Review
- Validation of de novo designed water-soluble and transmembrane β-barrels by in silico folding and melting.Protein science : a publication of the Protein Society · 2024Article
- Article
- The Effect of β-Sheet Secondary Structure on All-β Proteins by Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2024Article
- Diversifying de novo TIM barrels by hallucination.Protein science : a publication of the Protein Society · 2024Article
- The structural landscape of the immunoglobulin fold by large-scale de novo design.Protein science : a publication of the Protein Society · 2024Article
- Design of complicated all-α protein structures.Nature structural & molecular biology · 2024Article
- Review
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 4 countries.
Funding
Abstract
β-sheet proteins carry out critical functions in biology, and hence are attractive scaffolds for computational protein design. Despite this potential, de novo design of all-β-sheet proteins from first principles lags far behind the design of all-α or mixed-αβ domains owing to their non-local nature and the tendency of exposed β-strand edges to aggregate. Through study of loops connecting unpaired β-strands (β-arches), we have identified a series of structural relationships between loop geometry, side chain directionality and β-strand length that arise from hydrogen bonding and packing constraints on regular β-sheet structures. We use these rules to de novo design jellyroll structures with double-stranded β-helices formed by eight antiparallel β-strands. The nuclear magnetic resonance structure of a hyperthermostable design closely matched the computational model, demonstrating accurate control over the β-sheet structure and loop geometry. Our results open the door to the design of a broad range of non-local β-sheet protein structures.
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Identifiers
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.