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| license: mit |
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| # Data for MF-Design |
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| This repository hosts the datasets for the paper **"Repurposing AlphaFold3-like Protein Folding Models for Antibody Sequence and Structure Co-design" (MF-Design)**. |
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| The main code repository can be found at [MF-Design](https://github.com/yangnianzu0515/mfdesign). |
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| ## Directory Structure |
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| The `./data/` directory contains all the necessary data for running and evaluating the models. |
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| * **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`. |
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| Notably, the file `ccd.rdb` is sourced from the [Boltz-1](https://github.com/jwohlwend/boltz) repository. |
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| ## Citation |
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| If you use MFDesign in your research, please cite our paper: |
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| ```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)} |
| } |
