README.md

metadata

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.

Directory Structure

The ./model directory contains various trained model checkpoints.

The following files are sourced from the Boltz-1 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:

@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)}
}