Multiple Protein Docking with a Single Ligand

This repository provides a comprehensive guide and scripts to perform multiple protein docking with a single ligand on an HPC cluster. The aim is to help researchers and students understand and execute the process efficiently.

Table of Contents

1. Introduction
2. Folder Structure
3. Requirements
4. Installation
5. Usage
6. Contributing
7. License
8. Contact

Introduction

In computational biology, docking studies help predict the interaction between a ligand and a protein. This project automates the process of docking a single ligand with multiple protein targets using AutoDock Vina and an HPC cluster.

Folder Structure

• Generate_job: Scripts to generate job files for the HPC cluster.
• Ligand: Contains ligand files for docking.
• Log: Directory for log files generated during docking.
• Out: Output directory for docking results.
• Scripts: Helper scripts for various tasks.
• Submit_job: Scripts to submit jobs to the HPC cluster.
• Target: Contains protein target files.
• Vina: Configuration files and executables for AutoDock Vina.

Requirements

• Python 3.5 or higher
• AutoDock Vina
• HPC cluster access
• Git

Installation

1. Clone the repository:

   git clone https://github.com/your-username/multiple_protein_docking.git
   cd multiple_protein_docking
   

Usage

1. Prepare the ligand and protein target files:

   i. Place ligand files (already converted to pdbqt) in the Ligand directory.

   ii. Place protein target files (already converted to pdbqt) in the Target directory.

2. Generate the centre of masses for proteins:

   python com_calculator.py
   

3. Generate job files:

   python Generate_job/generate_jobs.py
   

4. Submit jobs to the HPC cluster:

   qsub Submit_job/submit_jobs.sh
   

5. Monitor log files and retrieve results:

Logs will be available in the Log directory. Results will be stored in the Out directory.

Contributing

Contributions are welcome! Please read the CONTRIBUTING.md file for guidelines on how to contribute to this project.

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 or contact ndolling5@gmail.com