The discovery of macrocyclic peptide therapeutics has been slow. We introduce RFpeptides, a deep learning method that enables the de novo design of macrocyclic peptide binders to therapeutic targets. The designed macrocycles bind their respective protein targets with high affinity and atomic-level accuracy.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$32.99 /Â 30Â days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout

References
Hosseinzadeh, P. et al. Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites. Nat. Commun. 12, 3384 (2021). This paper reports the design of macrocycle binders with physics-based methods.
MuratspahiÄ, E. et al. Design and structural validation of peptideâdrug conjugate ligands of the kappa-opioid receptor. Nat. Commun. 14, 8064 (2023). This paper reports the design of peptide binders against opioid receptors using physics-based methods.
Rettie, S. A. et al. Cyclic peptide structure prediction and design using AlphaFold2. Nat. Commun. 16, 4730 (2025). This paper presents a method to design macrocyclic peptides with AlphaFold2.
Watson, J. L. et al. De novo design of protein structure and function with RFdiffusion. Nature 620, 1089â1100 (2023). This paper introduces a denoising diffusion approach for protein design.
Krishna, R. et al. Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science 384, eadl2528 (2024). This paper presents an all-atom model for protein design and structure prediction.
Waskom, M. L. seaborn: statistical data visualization. J. Open Source Softw. 6, 3021 (2021).
Additional information
Publisherâs note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
This is a summary of: Rettie, S. A. et al. Accurate de novo design of high-affinity protein-binding macrocycles using deep learning. Nat. Chem. Biol. https://doi.org/10.1038/s41589-025-01929-w (2025).
Rights and permissions
About this article
Cite this article
Deep learning-enabled design of macrocyclic peptide binders. Nat Chem Biol (2025). https://doi.org/10.1038/s41589-025-02062-4
Published:
DOI: https://doi.org/10.1038/s41589-025-02062-4