ArticleProceedings of the National Academy of Sciences of the United States of America2020
An enumerative algorithm for de novo design of proteins with diverse pocket structures.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed, 87 citations in OpenAlex.
- Genetically encoded tools for tracking metabolites in live cells.Biochemical Society transactions · 2026Review
- A Hybrid Physics-Deep Learning Framework for Combinatorial De Novo Design of Small-Molecule Binding Proteins.bioRxiv : the preprint server for biology · 2026Article
- Using experimental results of protein design to guide biomolecular energy-function development.PLoS computational biology · 2026Article
- Small-molecule binding and sensing with a designed protein family.Nature communications · 2026Article
- Buttressing ligand-binding pockets in de novo designed NTF2-like domains.Protein science : a publication of the Protein Society · 2025Article
- An improved model for prediction of de novo designed proteins with diverse geometries.bioRxiv : the preprint server for biology · 2025Article
- Efficient Generation of Protein Pockets with PocketGen.bioRxiv : the preprint server for biology · 2024Article
- Neural network extrapolation to distant regions of the protein fitness landscape.Nature communications · 2024Article
- Review
- Machine learning for functional protein design.Nature biotechnology · 2024Review
- Sparks of function by de novo protein design.Nature biotechnology · 2024Review
- Design of complicated all-α protein structures.Nature structural & molecular biology · 2024Article
- Hallucination of closed repeat proteins containing central pockets.Nature structural & molecular biology · 2023Article
- Article
- Article
- Review
- De novo design of small beta barrel proteins.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Possibilities of Using De Novo Design for Generating Diverse Functional Food Enzymes.International journal of molecular sciences · 2023Review
- De novo design of luciferases using deep learning.Nature · 2023Article
- Design of Diverse Asymmetric Pockets inBiochemistry · 2023Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To create new enzymes and biosensors from scratch, precise control over the structure of small-molecule binding sites is of paramount importance, but systematically designing arbitrary protein pocket shapes and sizes remains an outstanding challenge. Using the NTF2-like structural superfamily as a model system, we developed an enumerative algorithm for creating a virtually unlimited number of de novo proteins supporting diverse pocket structures. The enumerative algorithm was tested and refined through feedback from two rounds of large-scale experimental testing, involving in total the assembly of synthetic genes encoding 7,896 designs and assessment of their stability on yeast cell surface, detailed biophysical characterization of 64 designs, and crystal structures of 5 designs. The refined algorithm generates proteins that remain folded at high temperatures and exhibit more pocket diversity than naturally occurring NTF2-like proteins. We expect this approach to transform the design of small-molecule sensors and enzymes by enabling the creation of binding and active site geometries much more optimal for specific design challenges than is accessible by repurposing the limited number of naturally occurring NTF2-like proteins.
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