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--- |
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title: B-cell Epitope Prediction Server |
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emoji: 🧬 |
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colorFrom: blue |
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colorTo: purple |
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sdk: gradio |
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sdk_version: 5.36.2 |
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app_file: app.py |
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pinned: false |
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license: mit |
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--- |
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# 🧬 B-cell Epitope Prediction Server |
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A web-based interface for B-cell epitope prediction using the ReCEP model. |
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## 📋 How to Use |
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### 1. Input Protein Structure |
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Choose one of two input methods: |
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#### Option A: PDB ID |
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- Enter a 4-character PDB ID (e.g., "5I9Q") |
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- Specify the chain ID (e.g., "A") |
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#### Option B: Upload PDB File |
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- Upload a PDB structure file (.pdb or .ent format) |
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- Optionally specify a custom PDB ID |
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- Specify the chain ID |
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### 2. Configure Prediction Parameters |
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#### Basic Parameters: |
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- **Chain ID**: Target protein chain (default: A) |
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#### Advanced Parameters (Optional): |
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- **Radius**: Spherical region radius in Ångstroms (default: 19.0) |
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- **Top-k Regions**: Number of top regions to analyze (default: 7) |
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- **Encoder**: Protein encoder type (ESM-C only now) |
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- **Device Configuration**: CPU or GPU processing (CPU Only now) |
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- **Threshold**: Custom prediction threshold (leave empty for auto, required) |
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### 3. View Results |
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The application provides: |
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#### Prediction Summary |
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- Protein information (PDB ID, chain, length, sequence) |
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- Prediction statistics (epitope count, coverage rate, etc.) |
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- Top-k region centers |
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- Predicted epitope residues |
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- Binding region residues |
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#### Download Options |
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- **JSON Results**: Complete prediction data with metadata |
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- **CSV Results**: Residue-level predictions for analysis |
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- **3D Visualization**: Interactive HTML file with 3Dmol.js viewer |
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### 4. 3D Visualization |
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The downloadable HTML file includes: |
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- **Display Modes**: |
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- Predicted Epitopes: Highlight predicted epitope residues |
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- Probability Gradient: Color residues by prediction confidence |
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- **Representation Styles**: Cartoon, Surface, Stick, Sphere |
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- **Interactive Controls**: Rotate, zoom, pan, reset view, save image |
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## 📜 License |
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This project is licensed under the MIT License - see the LICENSE file for details. |
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**Note**: This is a research tool for B-cell epitope prediction. Results should be validated through experimental methods for clinical or commercial applications. |
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