---
license: mit
---

# Models for MF-Design

This repository hosts the pre-trained model checkpoints for the paper **"Repurposing AlphaFold3-like Protein Folding Models for Antibody Sequence and Structure Co-design" (MF-Design)**.

The main code repository can be found at [MF-Design](https://github.com/yangnianzu0515/mfdesign).

## Directory Structure

The `./model` directory contains various trained model checkpoints.

The following files are sourced from the [Boltz-1](https://github.com/jwohlwend/boltz) repository:
* `boltz1.ckpt`
* `boltz1_conf.ckpt`
* `ccd.pkl`
* `symmetry.pkl`

We provide the following checkpoints for our MFDesign models:

* **MFDesign-D**: Checkpoints for all four training stages are provided.
* **MFDesign-C**: The checkpoint for the final stage is provided.

For the final stage of both `MFDesign-D` and `MFDesign-C`, we also provide an additional checkpoint for models that were trained without epitope information.

## Citation

If you use MFDesign in your research, please cite our paper:

```bibtex
@article{mf_design_2025,
  title={Repurposing AlphaFold3-like Protein Folding Models for Antibody Sequence and Structure Co-design},
  author={Nianzu Yang and Songlin Jiang and Jian Ma and Huaijin Wu and Shuangjia Zheng and Wengong Jin and Junchi Yan},
  journal={NeurIPS 2025},
  year={2025},
  url={[https://openreview.net/pdf?id=M96edY67nS)}
}