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.

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 repository.

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)}
}