---
license: mit
---

# Data for MF-Design

This repository hosts the datasets 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 `./data/` directory contains all the necessary data for running and evaluating the models.

* **Raw and Processed Data**: Includes the original data used for training in `./data/raw_data.tar.zst` and its processed versions in `./data/antibody_data.tar.zst` and `./data/msa.tar.zst`.
* **Dataset Split Files**: Files detailing the splits for the training, validation, and test sets in `*_entry.json`.
* **Test Set Inputs**: Input `yaml` files required for running inference on the test set in `./data/test_yaml_dir.tar.zst`.

Notably, the file `ccd.rdb` is sourced from the [Boltz-1](https://github.com/jwohlwend/boltz) repository.

## 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)}
}