ArticleNature2018
De novo design of a fluorescence-activating β-barrel.
Article in Nature, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 205 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
205 citing papers in PubMed, 370 citations in OpenAlex.
- Synthetic fluorescent proteins: Bridging advanced imaging technologies and clinical practice.Clinical and translational medicine · 2026Article
- Lighting Up Biology: GFP-Inspired Fluorescent Probes for Sensing and Imaging.Journal of the American Chemical Society · 2026Article
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- Emergence of specific binding and catalysis from a designed generalist binding protein.Nature chemistry · 2026Article
- Review
- Modular Input-Output Biosensor Design UsingACS sensors · 2026Article
- Limitations of the refolding pipeline for de novo protein design.Protein science : a publication of the Protein Society · 2026Article
- De Novo Design and Directed Evolution Refinement of Mirror-Image Protein Binders Targeting Interleukin-4.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- De novo design of a macrocycle-induced dimerization system for cellular control.Nature communications · 2026Article
- Molecular rotor-based probes for protein monitoring in biomedical research.Nature reviews. Chemistry · 2026Review
- De novo design of a macrocycle induced dimerization system for cellular control.bioRxiv : the preprint server for biology · 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
- Using experimental results of protein design to guide biomolecular energy-function development.PLoS computational biology · 2026Article
- Review
- Small-molecule binding and sensing with a designed protein family.Nature communications · 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
- Unsymmetric bimetallic centres in metalloproteins and synthetic models.Nature reviews. Chemistry · 2026Review
- β-barrels from short macrocyclic peptides.Chemical communications (Cambridge, England) · 2026Article
- Protein folding stability estimation with explicit consideration of unfolded states.Nature communications · 2026Article
145 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
18 authors at 5 institutions in 2 countries.
Funding
Abstract
The regular arrangements of β-strands around a central axis in β-barrels and of α-helices in coiled coils contrast with the irregular tertiary structures of most globular proteins, and have fascinated structural biologists since they were first discovered. Simple parametric models have been used to design a wide range of α-helical coiled-coil structures, but to date there has been no success with β-barrels. Here we show that accurate de novo design of β-barrels requires considerable symmetry-breaking to achieve continuous hydrogen-bond connectivity and eliminate backbone strain. We then build ensembles of β-barrel backbone models with cavity shapes that match the fluorogenic compound DFHBI, and use a hierarchical grid-based search method to simultaneously optimize the rigid-body placement of DFHBI in these cavities and the identities of the surrounding amino acids to achieve high shape and chemical complementarity. The designs have high structural accuracy and bind and fluorescently activate DFHBI in vitro and in Escherichia coli, yeast and mammalian cells. This de novo design of small-molecule binding activity, using backbones custom-built to bind the ligand, should enable the design of increasingly sophisticated ligand-binding proteins, sensors and catalysts that are not limited by the backbone geometries available in known protein structures.
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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.