https://github.com/amarkar7/autodockvina_batchdocking
A complete step-by-step pipeline to dock multiple ligands using AutoDock Vina. Includes ligand preparation, file format conversion, batch docking, and result extraction.
https://github.com/amarkar7/autodockvina_batchdocking
autodock-vina bioinformatics docking molecular-docking openbabel perl rdkit shell virtual-screening
Last synced: 27 days ago
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A complete step-by-step pipeline to dock multiple ligands using AutoDock Vina. Includes ligand preparation, file format conversion, batch docking, and result extraction.
- Host: GitHub
- URL: https://github.com/amarkar7/autodockvina_batchdocking
- Owner: Amarkar7
- License: mit
- Created: 2025-07-17T16:37:21.000Z (3 months ago)
- Default Branch: main
- Last Pushed: 2025-07-17T16:52:07.000Z (3 months ago)
- Last Synced: 2025-07-17T19:28:43.460Z (3 months ago)
- Topics: autodock-vina, bioinformatics, docking, molecular-docking, openbabel, perl, rdkit, shell, virtual-screening
- Language: Python
- Homepage:
- Size: 13.7 KB
- Stars: 1
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# AutoDock Vina: Batch Docking Workflow for Multiple Ligands
This repository provides a complete pipeline for high-throughput molecular docking of multiple ligands to a single receptor using **AutoDock Vina**. The workflow includes:
1. Protein preparation using Autodock
2. Ligand cleaning and 3D conformer generation using RDKit
3. Format conversion to `.pdbqt` using OpenBabel
4. Automated docking using a Perl script
5. Extraction of top 5 ligands with the best binding affinities
## Requirements
Install the following:
```bash
conda create -n vina_env python=3.9 rdkit openbabel -c conda-forge
conda activate vina_env
sudo apt install autodock-vina
# AutoDockVina_BatchDocking
A complete step-by-step pipeline to dock multiple ligands using AutoDock Vina. Includes ligand preparation, file format conversion, batch docking, and result extraction.