ArticleScience (New York, N.Y.)2020
A defined structural unit enables de novo design of small-molecule-binding proteins.
Article in Science (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed, 138 citations in OpenAlex.
- Design-Evolution Synergy Enables New-to-Nature Enzyme Chemistry.bioRxiv : the preprint server for biology · 2026Article
- Genetically encoded tools for tracking metabolites in live cells.Biochemical Society transactions · 2026Review
- Article
- AbioRxiv : the preprint server for biology · 2026Article
- Redesign of the Ferritin Ferroxidase Center for Universal Molecular Binding or Specific Recognition.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Emergence of specific binding and catalysis from a designed generalist binding protein.Nature chemistry · 2026Article
- De Novo Design of Near-Infrared Fluorescence-Activating Proteins.Journal of the American Chemical Society · 2026Article
- Advancing protein engineering via organic chemistry.Communications chemistry · 2026Review
- A Hybrid Physics-Deep Learning Framework for Combinatorial De Novo Design of Small-Molecule Binding Proteins.bioRxiv : the preprint server for biology · 2026Article
- Review
- Small-molecule binding and sensing with a designed protein family.Nature communications · 2026Article
- From single step hops to emergent biological phenomena.Journal of inorganic biochemistry · 2026Review
- AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2.Nature methods · 2026Article
- Deciphering DEL pocket patterns through contrastive learning.Nature communications · 2026Article
- De novo protein design: a transformative frontier in clinical protein applications.Journal of translational medicine · 2026Review
- Computational design of dynamic biosensors for emerging synthetic opioids.Nature communications · 2026Article
- AI-Driven De Novo Binder Design: From Structure Prediction to Closed-Loop Optimization.Computational and structural biotechnology journal · 2026Review
- Exploring the Blueprint of Life: The Innovation in Antibody and Protein Design.Combinatorial chemistry & high throughput screening · 2026Article
- Article
- Discovery and artificial intelligence-guided mechanistic elucidation of a narrow-spectrum antibiotic.Nature microbiology · 2025Article
19 more citing papers are in PubMed but not listed here.
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2 authors at 1 institution in 1 country.
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Abstract
The de novo design of proteins that bind highly functionalized small molecules represents a great challenge. To enable computational design of binders, we developed a unit of protein structure-a van der Mer (vdM)-that maps the backbone of each amino acid to statistically preferred positions of interacting chemical groups. Using vdMs, we designed six de novo proteins to bind the drug apixaban; two bound with low and submicromolar affinity. X-ray crystallography and mutagenesis confirmed a structure with a precisely designed cavity that forms favorable interactions in the drug-protein complex. vdMs may enable design of functional proteins for applications in sensing, medicine, and catalysis.
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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.