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sars-cov-2-mpro-drug-discovery

A complete virtual screening + QSAR modeling + ADME profiling project

https://github.com/basemmak/sars-cov-2-mpro-drug-discovery

Science Score: 44.0%

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Repository

A complete virtual screening + QSAR modeling + ADME profiling project

Basic Info
  • Host: GitHub
  • Owner: basemmak
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 6.84 KB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created 9 months ago · Last pushed 9 months ago
Metadata Files
Readme Citation

README.md

🧬 SARS-CoV-2 Mpro Drug Discovery Project

This repository presents a full Computer-Aided Drug Design (CADD) workflow for identifying potential inhibitors of the Main Protease (Mpro) of SARS-CoV-2. The study combines molecular docking, QSAR modeling, and ADME/Tox screening of candidate ligands such as Aspirin, Curcumin, and related compounds.

📌 Project Objectives

  • Prepare ligands using SMILES and generate 3D conformers.
  • Perform molecular docking using AutoDock Vina.
  • Build and evaluate QSAR models for pIC50 prediction.
  • Screen ADME and toxicity profiles using SwissADME and pkCSM.
  • Visualize protein-ligand interactions and model performance.

📁 Repository Structure

SARS-CoV-2-Mpro-Drug-Discovery/ ├── notebooks/ │ ├── 1_ligand_preparation.ipynb │ ├── 2_docking_pipeline.ipynb │ ├── 3_qsar_modeling.ipynb │ └── 4_adme_screening.ipynb ├── data/ │ ├── ligands/ # SMILES, PDBQT files │ ├── protein/ # 6LU7.pdb │ └── docking_results/ ├── media/ # Plots and visualizations ├── requirements.txt ├── LICENSE └── README.md

🛠️ Tools & Libraries

  • RDKit – Cheminformatics and descriptor calculation
  • Open Babel – File conversion (.smi to .pdbqt)
  • AutoDock Vina – Molecular docking
  • scikit-learn – Machine learning for QSAR
  • SwissADME / pkCSM – ADME/Tox prediction
  • PyMOL / Chimera – Visualization

🚀 How to Run

```bash

Install dependencies

pip install -r requirements.txt

Run each notebook in order

cd notebooks jupyter notebook ```

👤 Author

Basem Abdelrahman
Bioinformatics Advanced Diploma – LLRI
GitHub Profile

📄 License

This project is licensed under the MIT License.

Owner

  • Name: Basem Abdelrahman
  • Login: basemmak
  • Kind: user
  • Location: المملكة العربية السعودية
  • Company: AIS

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this project, please cite it as below."
authors:
  - family-names: Abdelrahman
    given-names: Basem
title: "Structure-Based Virtual Screening and QSAR Analysis for SARS-CoV-2 Mpro Inhibitors"
version: 1.0.0
date-released: 2025-05-24
license: MIT
repository-code: https://github.com/basemmak/SARS-CoV-2-Mpro-Drug-Discovery

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Dependencies

SARS-CoV-2-Mpro-Drug-Discovery/SARS-CoV-2-Mpro-Drug-Discovery/requirements.txt pypi
requirements.txt pypi
  • matplotlib *
  • numpy *
  • openbabel-wheel *
  • pandas *
  • rdkit-pypi *
  • requests *
  • scikit-learn *
  • seaborn *