Virtual Screening Script using Unidock (Autodock Vina-GPU)

This script automates virtual screening using the Unidock docking tool, leveraging GPU acceleration for fast computations.

Prerequisites

To use this script, ensure the following:

1. System Requirements:

   • A system with a compatible GPU card.
   • CUDA must be installed and configured.
   • Examples of supported GPUs:
     • NVIDIA RTX 30 series (e.g., RTX 3060, RTX 3080)
     • NVIDIA RTX 20 series (e.g., RTX 2060, RTX 2080)
     • NVIDIA Tesla series (e.g., Tesla V100, Tesla A100)
   • Ensure the correct version of CUDA for your GPU driver.

2. Unidock Installation:

   • Install Unidock, which is optimized for GPU-based docking.
   • Follow the official Unidock installation guide for setup.

3. Protein File:

   • The receptor protein file should be named receptor.pdbqt.
   • Place the file in the same directory as the script.

4. Ligands Folder:

   • All ligand files should be placed in the ligands folder.
   • Ligands must be in .pdbqt format.

5. Configuration File:

   • The script uses a configuration file named config.txt.
   • Ensure the file includes the following parameters:

     center_x = -24.247
     center_y = 11.918
     center_z = 11.502
     size_x = 30
     size_y = 30
     size_z = 30
     

   • Note: The search box size should not exceed 30 units for size_x, size_y, and size_z.

6. Usage:

   1. Clone or download the script to your local system.
   2. Place the receptor.pdbqt file in the script's directory.
   3. Ensure all ligand files are in the ligands folder and are in .pdbqt format.
   4. Verify the config.txt file is properly configured as shown above.
   5. Run the screening script:

      bash unidock_vina_screen.sh

   6. The results will be saved in the results directory.

7. Sorting and Selecting Top Ligands:

   To sort the results and extract top ligands, use the sorting script:

   bash unidock_sort.sh

   • The script prompts the user to specify the number of top ligands to extract.
   • Results are saved in sorted_results.csv and sorted_results.txt.
   • Top ligands are copied to the Top_ligands directory.

Output

• For each ligand, a result file with docking details will be created in the results folder.
• The script prints progress updates for each ligand processed.

Additional Notes

• Ensure proper permissions for executing the script (chmod +x script_name.sh).
• GPU memory issues may arise if too many ligands are processed at once. Consider splitting the ligand files if needed.
• For optimal performance, ensure all dependencies are correctly installed and the GPU drivers are up to date.

Citation

If you are using this script for your studies, kindly acknowledge the use of Open Babel as per its citation guidelines and mention my GitHub repository:

Yu, Yuejiang, et al. "Uni-Dock: GPU-accelerated docking enables ultralarge virtual screening." Journal of chemical theory and computation 19.11 (2023): 3336-3345. https://doi.org/10.1021/acs.jctc.2c01145

Trott, Oleg, and Arthur J. Olson. "AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading." Journal of computational chemistry 31.2 (2010): 455-461. https://doi.org/10.1002/jcc.21334

For the latest version of this script and updates, visit my GitHub repository: https://github.com/Gopinath-Murugan/Unidock-Vina-screening

Mentioning this repository in your publications or research would be greatly appreciated.

Happy docking and sorting!