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# 🧬 AbLang2 Sequence Restorer - Hugging Face Spaces
This is a Gradio web application that provides the AbLang2 sequence restoration utility through Hugging Face Spaces.
## 🎯 What it does
The AbLang2 Sequence Restorer allows you to:
- **Restore masked residues** (*) in antibody sequences
- **Work with paired sequences** (heavy and light chains)
- **Handle single chains** (heavy or light chain only)
- **Use alignment** for variable missing lengths
## 🚀 How to use
1. **Enter sequences**: Provide heavy chain, light chain, or both sequences
2. **Mask residues**: Use `*` to indicate residues you want to restore
3. **Choose alignment**: Enable "Use Alignment" for variable missing lengths
4. **Get results**: Click "Restore Sequences" to get the restored antibody sequences
## 📝 Example Usage
### Example 1: Both chains with masked residues
- **Heavy Chain**: `EVQ***SGGEVKKPGASVKVSCRASGYTFRNYGLTWVRQAPGQGLEWMGWISAYNGNTNYAQKFQGRVTLTTDTSTSTAYMELRSLRSDDTAVYFCAR**PGHGAAFMDVWGTGTTVTVSS`
- **Light Chain**: `DIQLTQSPLSLPVTLGQPASISCRSS*SLEASDTNIYLSWFQQRPGQSPRRLIYKI*NRDSGVPDRFSGSGSGTHFTLRISRVEADDVAVYYCMQGTHWPPAFGQGTKVDIK`
### Example 2: Heavy chain only
- **Heavy Chain**: `EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMGWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDY**GMDVWGQGTTVTVSS`
- **Light Chain**: (leave empty)
## 🔧 Technical Details
- **Model**: AbLang2 from Hugging Face Hub (`hemantn/ablang2`)
- **Framework**: Gradio for the web interface
- **Backend**: PyTorch with Transformers library
- **Processing**: Automatic GPU acceleration when available
## 📚 Related Resources
- **Original AbLang2**: [https://github.com/TobiasHeOl/AbLang2](https://github.com/TobiasHeOl/AbLang2)
- **Model Repository**: [https://huggingface.co/hemantn/ablang2](https://huggingface.co/hemantn/ablang2)
- **Full Documentation**: See the main README.md for comprehensive usage examples
## 🤝 Citation
If you use this tool in your research, please cite the original AbLang2 paper:
```
@article{Olsen2024,
title={Addressing the antibody germline bias and its effect on language models for improved antibody design},
author={Tobias H. Olsen, Iain H. Moal and Charlotte M. Deane},
journal={bioRxiv},
doi={https://doi.org/10.1101/2024.02.02.578678},
year={2024}
}
``` |