GenXDrug - NVIDIA Bio AI Tools

Overview

GenXDrug is a comprehensive web application that integrates multiple NVIDIA Bio AI tools for molecular and biological sequence analysis. The application provides a user-friendly interface for protein structure prediction, molecular generation, biological sequence analysis, and molecular docking.

Live Demo

Check out the live demo of GenXDrug: GenXDrug MVP

Features

1. Protein Structure Prediction (AlphaFold2)

• Input protein sequences for 3D structure prediction
• Visualize predicted protein structures
• Download PDB files
• Advanced parameter customization

2. Molecular Generation (GenMol)

• Generate novel molecules from scratch
• Generate molecules based on input SMILES
• Visualize generated molecules
• Analyze generation statistics
• Download generated structures

3. BioNeMo (Biological Sequence Analysis)

• Analyze DNA, RNA, and protein sequences
• Perform GC content analysis
• Analyze amino acid composition
• Predict secondary structures
• Identify sequence motifs
• Visualize sequence alignments
• Perform phylogenetic analysis

4. Molecular Docking (DiffDock)

• Upload protein and ligand files
• Run docking simulations
• Visualize docking results
• Analyze binding poses
• Download docking results

5. AI Assistant

• Get help and guidance
• Answer questions about tools
• Provide bioinformatics insights
• Troubleshoot issues

Architecture

UI/UX Design

Installation

1. Clone the repository:

git clone https://github.com/tiwariar7/genxdrug.git
cd genxdrug

2. Install dependencies:

pip install -r requirements.txt

3. Create a config.py file with your API keys:

API_KEYS = {
    "alphafold": "your_alphafold_api_key",
    "genmol": "your_genmol_api_key",
    "bionemo": "your_bionemo_api_key",
    "diffdock": "your_diffdock_api_key",
    "gemini": "your_gemini_api_key"
}

4. Run the application:

streamlit run app.py

Troubleshooting

Common Issues and Solutions

1. API Key Errors

   • Issue: "Invalid API key" or "API key not found" errors
   • Solution:
     • Verify that your API keys are correctly formatted in config.py
     • Ensure there are no extra spaces or special characters
     • Check if the API keys are still valid and not expired
     • Make sure the config.py file is in the correct directory

2. Dependency Installation Issues

   • Issue: Error during pip install -r requirements.txt
   • Solution:
     • Try installing dependencies one by one
     • Use a virtual environment
     • For RDKit installation issues:

       conda install -c conda-forge rdkit

     • For Py3DMol issues:

       pip install py3dmol

3. Streamlit Connection Issues

   • Issue: "Connection refused" or "Cannot connect to Streamlit"
   • Solution:
     • Check if port 8501 is available
     • Try running with a different port:

       streamlit run app.py --server.port 8502

     • Ensure no firewall is blocking the connection

4. Visualization Problems

   • Issue: 3D molecule viewer not working
   • Solution:
     • Clear browser cache
     • Try a different browser
     • Ensure WebGL is enabled in your browser
     • Check if all required JavaScript libraries are loaded

5. File Upload Issues

   • Issue: Cannot upload PDB or SDF files
   • Solution:
     • Verify file format is correct
     • Check file size (should be under Streamlit's limit)
     • Ensure file is not corrupted
     • Try converting file to a different format if needed

6. Memory Issues

   • Issue: Application crashes or runs slowly
   • Solution:
     • Increase Streamlit's memory limit:

       streamlit run app.py --server.maxUploadSize=500

     • Close other memory-intensive applications
     • Use smaller input files when possible

7. Browser Compatibility

   • Issue: UI elements not displaying correctly
   • Solution:
     • Use the latest version of Chrome, Firefox, or Edge
     • Disable browser extensions that might interfere
     • Clear browser cache and cookies

8. API Rate Limiting

   • Issue: "Too many requests" error
   • Solution:
     • Wait before making new requests
     • Contact NVIDIA support for higher rate limits
     • Implement request queuing in your code

If you encounter any other issues, please:

1. Check the Streamlit logs for error messages
2. Verify your system meets the minimum requirements
3. Try restarting the application
4. Open an issue in the GitHub repository with:
   • Error message
   • Steps to reproduce
   • System information
   • Screenshots if applicable

API Keys

The application requires the following API keys:

• NVIDIA AlphaFold2 API key
• NVIDIA GenMol API key
• NVIDIA BioNeMo API key
• NVIDIA DiffDock API key
• Google Gemini API key

Dependencies

• streamlit
• requests
• numpy
• pandas
• matplotlib
• rdkit
• py3Dmol
• biopython
• plotly
• google-generativeai

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contact

For any questions or suggestions, please open an issue in the GitHub repository.

Acknowledgments

• NVIDIA for providing the Bio AI tools
• Streamlit for the web framework
• All contributors and users of the application