> ## Documentation Index
> Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt
> Use this file to discover all available pages before exploring further.
# FreeBindCraft Binder Design
> PyRosetta-free de novo protein binder design against a target (FreeBindCraft).
**License:** FreeBindCraft uses MIT for code and CC-BY-4.0 for model weights and may require explicit attribution when utilized. Please refer to the [code license](https://github.com/cytokineking/FreeBindCraft/blob/master/LICENSE) and [model weights license](https://github.com/google-deepmind/alphafold#model-parameters-license) for full terms.
This generator is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.
```bibtex theme={null}
@article{pacesa2025bindcraft,
title={One-shot design of functional protein binders with BindCraft},
author={Pacesa, Martin and Nickel, Lennart and Schellhaas, Christian and Schmidt, Joseph and Pyatova, Ekaterina and Kissling, Lucas and Barendse, Patrick and Choudhury, Jagrity and Kapoor, Srajan and Alcaraz-Serna, Ana and Cho, Yehlin and Ghamary, Kourosh H. and Vinu{\'e}, Laura and Yachnin, Brahm J. and Wollacott, Andrew M. and Buckley, Stephen and Westphal, Adrie H. and Lindhoud, Simon and Georgeon, Sandrine and Goverde, Casper A. and Hatzopoulos, Georgios N. and G{\"o}nczy, Pierre and Muller, Yannick D. and Schwank, Gerald and Swarts, Daan C. and Vecchio, Alex J. and Schneider, Bernard L. and Ovchinnikov, Sergey and Correia, Bruno E.},
journal={Nature},
volume={646},
number={8084},
pages={483--492},
year={2025},
month={Aug},
publisher={Springer Science and Business Media LLC},
doi={10.1038/s41586-025-09429-6},
issn={1476-4687}
}
@misc{freebindcraft2025,
title={FreeBindCraft: BindCraft with optional, PyRosetta-free scoring and relaxation},
author={{cytokineking} and {FreeBindCraft contributors}},
year={2025},
howpublished={\url{https://github.com/cytokineking/FreeBindCraft}},
note={MIT-licensed fork of BindCraft replacing PyRosetta with OpenMM, FreeSASA, and sc-rs}
}
```
De novo protein binder generator using the PyRosetta-free FreeBindCraft pipeline.
Hallucinates a binder against a frozen target with AlphaFold2, refines it with ProteinMPNN,
re-validates with AlphaFold2, and scores the interface with OpenMM/FreeSASA/sc-rs. The assigned
segment's length is the binder length, and its proposal count is the number of designs requested.
Each accepted design's sequence, predicted complex, and metrics are written onto a proposal; if
the pipeline returns fewer designs than requested, the proposal pool is truncated to what it
produced, and an empty result raises.
## API Reference
Configuration object for FreeBindCraftGenerator.
Bundles the target specification with the full FreeBindCraft pipeline settings. The binder
length and the number of designs are NOT set here — they are derived from the assigned segment
(length = the segment's length; one design per proposal slot) at sample time.
Target to design a binder against (file path, PDB/CIF content, or Structure).
Chain ID(s) of the frozen target (comma-separated for multi-chain).
Comma-separated 1-indexed target residues the binder must contact (e.g. '1-10,56').
Filename prefix recorded on each accepted design.
FreeBindCraft pipeline settings; the program seed overrides its seed field.
evo-design/proto-language/proto\_language/generator/freebindcraft\_generator.py
dguo8412