Citation & License

Cite and share this work.

If Cyclic BindCraft helps your research, please cite all three entries below. The combined work inherits two BSD-3-Clause upstream licenses; the new cyclic-patch code is also BSD-3-Clause.

How to cite

Three citations.

If you use Cyclic BindCraft in published research, please cite all three of the following.

1. BindCraft — the base pipeline

doi.org/10.1038/s41587-024-02428-6

Pacesa, M., Pei, A., Sesterhenn, F. et al.

BindCraft: one-shot design of functional protein binders. Nature Biotechnology (2025). bioRxiv preprint: doi:10.1101/2024.09.30.615802.

2. RFpeptide — the cyclization technique

doi.org/10.1038/s41589-025-01929-w

Rettie, S. A., Juergens, D., Adebomi, V. et al.

RFpeptides: an RFdiffusion-based method for designing macrocyclic peptide binders. Nature Chemical Biology 21, 1948–1956 (2025).

3. Cyclic BindCraft modification (this work)

Repository (TBD)

Tarkashvand, A., Roohi, A.

Please cite the Cyclic BindCraft release DOI (to be assigned on Zenodo upon publication) and reference the documentation set at /docs/.

BibTeX entries

citation.bib
@article{pacesa2025bindcraft,
  title   = {BindCraft: one-shot design of functional protein binders},
  author  = {Pacesa, Martin and others},
  journal = {Nature Biotechnology},
  year    = {2025},
  doi     = {10.1038/s41587-024-02428-6}
}

@article{rettie2025rfpeptides,
  title   = {RFpeptides: an RFdiffusion-based method for designing
             macrocyclic peptide binders},
  author  = {Rettie, Samuel A. and Juergens, David and Adebomi, Victor and others},
  journal = {Nature Chemical Biology},
  volume  = {21}, pages = {1948--1956}, year = {2025},
  doi     = {10.1038/s41589-025-01929-w}
}

@software{cyclic_bindcraft,
  title        = {Cyclic {BindCraft}: Head-to-tail cyclic binder design by
                  porting {RFpeptide}'s cyclization into {BindCraft}},
  author       = {Tarkashvand, Ali and Roohi, Amirali},
  year         = {2025},
  url          = {https://github.com/TBD/cyclic-bindcraft}
}

Author lists

The author lists above are abbreviated — please use the official citation entries from the journal pages when preparing your manuscript.

License

Six components, one combined work.

Cyclic BindCraft is a derivative work that combines code from two BSD-3-Clause–licensed projects. The combined work inherits both upstream licenses; the new cyclic-patch code is released under BSD-3-Clause.

ComponentLicenseNotes
BindCraft (base pipeline)BSD-3-ClauseCopyright © 2024 Martin Pacesa and BindCraft contributors. Full text at repo/LICENSE.
RFdiffusion / RFpeptides branchBSD-3-Clause + additional clause on model weightsCyclic BindCraft does not redistribute RFdiffusion code or weights — it re-implements the cyclic encoding (~50 lines of JAX) from the published description. The rfpeptides branch remains an optional dependency for second-pass validation.
PyRosettaPyRosetta LicenseFree for academic/non-commercial; commercial requires Rosetta commercial license. Register at els2.comotion.uw.edu/product/pyrosetta. Not redistributed.
AlphaFold2 parametersCC BY 4.0 (DeepMind)Source code Apache 2.0. Unmodified.
ColabDesignMITCyclic patch is a derivative but does not redistribute ColabDesign source.
Cyclic BindCraft patch codeBSD-3-ClauseNew files: functions/cyclic_utils.py, modifications to colabdesign_utils.py / pyrosetta_utils.py / biopython_utils.py / generic_utils.py, and new JSON presets.

BSD-3-Clause excerpt

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: (1) retain the copyright notice and disclaimer; (2) reproduce the notice in binary distributions; (3) neither the name of the copyright holder nor contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED "AS IS" …

See repo/LICENSE for the full text.

Acknowledgements

Standing on the shoulders of giants.

Cyclic BindCraft would not exist without:

  • Martin Pacesa and the BindCraft team for the AF2-hallucination backbone, the add_termini_distance_loss hook that became the anchor for the cyclic bond loss, and the clean three-JSON config system.
  • Samuel Rettie, David Juergens, and the RFpeptide team for the elegant demonstration that ~50 lines of cyclic positional encoding is sufficient for macrocyclic peptide design — and for publishing the technique in enough detail to port.
  • Sergey Ovchinnikov and the ColabDesign team for the differentiable AF2 framework.
  • The RosettaCommons and PyRosetta teams for FastRelax, DeclareBond, InterfaceAnalyzerMover, and decades of protein-design infrastructure.
  • The IPD at the University of Washington for hosting the AfCycDesign and RF2-cyclic reference implementations we recommend for second-pass validation.

Papers

Reference papers.

NATURE BIOTECHNOLOGY · 2025

BindCraft: one-shot design of functional protein binders

Pacesa, Pei, Sesterhenn et al.

The base pipeline — AF2 hallucination + ProteinMPNN + PyRosetta FastRelax + JSON-driven filters. Cyclic BindCraft inherits this architecture unchanged.

doi.org/10.1038/s41587-024-02428-6

NATURE CHEMICAL BIOLOGY · 2025

RFpeptides: an RFdiffusion-based method for designing macrocyclic peptide binders

Rettie, Juergens, Adebomi et al.

The cyclization technique — cyclic 2-D relative positional encoding + cyclic bonded edge. ~50 lines of PyTorch. We port it as JAX in cyclize_relpos + cyclic_bonded_edges.

doi.org/10.1038/s41589-025-01929-w

bioRxiv · 2024

BindCraft preprint

The bioRxiv preprint of the BindCraft paper — describes the 4-stage design algorithm and the loss function in detail. Cite the published version above; this is for reference.

doi.org/10.1101/2024.09.30.615802

SOFTWARE · 2025

Cyclic BindCraft release (this work)

The modified-code patch against BindCraft v1.5.3. Zenodo DOI to be assigned on publication. Source: /modified-code/.

Repository (TBD)

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