| # 🧬 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} | |
| } | |
| ``` |