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| title: BroteinShake BioHub | |
| emoji: 🥤 | |
| colorFrom: green | |
| colorTo: gray | |
| sdk: docker | |
| app_port: 7860 | |
| pinned: false | |
| # BroteinShake | |
| AI-Driven Structural Mimicry & BBB-Shuttle Design | |
| A Gradio application for protein redesign using ProteinMPNN and structural refinement with OpenMM. | |
| ## Features | |
| 1. **Sequence Generation**: Download PDB structures and generate optimized sequences using ProteinMPNN | |
| 2. **Structural Refinement**: Refine ESM-folded structures with alignment and clash resolution | |
| ## Usage | |
| 1. Enter a PDB ID (e.g., 3kas) | |
| 2. Specify fixed chains (to keep unchanged) and variable chains (to redesign) | |
| 3. Generate sequences and fold the best design on ESM Atlas | |
| 4. Upload the folded structure for refinement | |
| ## Requirements | |
| - Python 3.10 | |
| - Conda environment with OpenMM and PDBFixer | |
| - ProteinMPNN (cloned automatically) | |
| ## Installation | |
| The space uses conda environment specified in `environment.yml`. | |