ArticleScience (New York, N.Y.)2024
De novo design of drug-binding proteins with predictable binding energy and specificity.
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 41 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
41 citing papers in PubMed.
- Deep learning based design of buried hydrogen bond networks with HBDesigner.bioRxiv : the preprint server for biology · 2026Article
- Article
- AbioRxiv : the preprint server for biology · 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
- De Novo Design of Near-Infrared Fluorescence-Activating Proteins.Journal of the American Chemical Society · 2026Article
- Protein design and RNA design: Perspectives.Quantitative biology (Beijing, China) · 2026Article
- Niraparib in breast cancer: evidence-based perspective on translational progress.Breast cancer (Tokyo, Japan) · 2026Review
- A Hybrid Physics-Deep Learning Framework for Combinatorial De Novo Design of Small-Molecule Binding Proteins.bioRxiv : the preprint server for biology · 2026Article
- Sequence Display enables large-scale sequence-activity datasets for rapid protein evolution.Nature biotechnology · 2026Article
- Review
- Quercetin upregulates steroid hormone biosynthesis to enhance reproductive performance in roosters.Poultry science · 2026Article
- Design of miniprotein inhibitors targeting complement C9 to block membrane attack complex assembly.Nature communications · 2026Article
- MutPPI+: a multimodal framework for predicting mutation effects on protein-protein interactions via mutation-path-based data augmentation.Briefings in bioinformatics · 2026Article
- AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2.Nature methods · 2026Article
- High-sensitivity, protein-independent detection of dsDNA sequences.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
- Bioswitches: Towards programmable, on-demand control of therapeutic proteins.Clinical and translational medicine · 2026Article
- Assessing structural prediction accuracy for nanobody-small molecule complexes.Protein engineering, design & selection : PEDS · 2026Article
- BoltzGen: Toward Universal Binder Design.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
- Update of
Authors and funding
14 authors.
Funding
Abstract
The de novo design of small molecule-binding proteins has seen exciting recent progress; however, high-affinity binding and tunable specificity typically require laborious screening and optimization after computational design. We developed a computational procedure to design a protein that recognizes a common pharmacophore in a series of poly(ADP-ribose) polymerase-1 inhibitors. One of three designed proteins bound different inhibitors with affinities ranging from <5 nM to low micromolar. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free energy calculations performed directly on the designed models were in excellent agreement with the experimentally measured affinities. We conclude that de novo design of high-affinity small molecule-binding proteins with tuned interaction energies is feasible entirely from computation.
Indexed as
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.