ArticleScience (New York, N.Y.)2024
Binding and sensing diverse small molecules using shape-complementary pseudocycles.
Article in Science (New York, N.Y.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Accelerating protein design by scaling experimental characterization.Nature communications · 2026Article
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- AbioRxiv : the preprint server for biology · 2026Article
- AI-GuidedJournal of the American Chemical Society · 2026Article
- Emergence of specific binding and catalysis from a designed generalist binding protein.Nature chemistry · 2026Article
- Redesign of the Ferritin Ferroxidase Center for Universal Molecular Binding or Specific Recognition.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Modular Input-Output Biosensor Design UsingACS sensors · 2026Article
- Tools For Building Artificial Biological Nanostructures.ACS nano · 2026Review
- Nondestructive tracking of viral infections by viral protein-initiated fluorescent sensors.Journal of virology · 2026Article
- A Hybrid Physics-Deep Learning Framework for Combinatorial De Novo Design of Small-Molecule Binding Proteins.bioRxiv : the preprint server for biology · 2026Article
- AI-Assisted Molecular Biosensors: Design Strategies for Wearable and Real-Time Monitoring.International journal of molecular sciences · 2026Review
- Review
- Small-molecule binding and sensing with a designed protein family.Nature communications · 2026Article
- Single-molecule peptide sequencing through reverse translation of peptides into DNA.Nature biotechnology · 2026Article
- Mesostructured Water Enhances Stability of ProteinMPNN-Designed Ubiquitin-Fold Proteins.Journal of the American Chemical Society · 2026Article
- De novo protein design: a transformative frontier in clinical protein applications.Journal of translational medicine · 2026Review
- Bioswitches: Towards programmable, on-demand control of therapeutic proteins.Clinical and translational medicine · 2026Article
- Stimuli-triggered formation ofCell biomaterials · 2026Article
- Assessing structural prediction accuracy for nanobody-small molecule complexes.Protein engineering, design & selection : PEDS · 2026Article
- Protein engineering: status report.Protein engineering, design & selection : PEDS · 2026Review
Corrections and comments
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Authors and funding
25 authors.
Funding
Abstract
We describe an approach for designing high-affinity small molecule-binding proteins poised for downstream sensing. We use deep learning-generated pseudocycles with repeating structural units surrounding central binding pockets with widely varying shapes that depend on the geometry and number of the repeat units. We dock small molecules of interest into the most shape complementary of these pseudocycles, design the interaction surfaces for high binding affinity, and experimentally screen to identify designs with the highest affinity. We obtain binders to four diverse molecules, including the polar and flexible methotrexate and thyroxine. Taking advantage of the modular repeat structure and central binding pockets, we construct chemically induced dimerization systems and low-noise nanopore sensors by splitting designs into domains that reassemble upon ligand addition.
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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.