Molecular Docking
Internal training, University of Medicine and Pharmacy at Ho Chi Minh city, Department of Organic Chemistry, 2022
This is a set of two (2+) tutorials on basic information of molecular docking incoporating python framework, using the Google Colab free cloud-computing environment in Fall 2022.
Introduction
These tutorials were created between Aug-Dec 2022 as part of the MedAI Training Session 2 for full execution over Google Colab and remote accesibility via web browsers. Each tutorial includes a brief introduction of the activities to be performed, installation instructions of the open-source software to be used in each session and several programming, visualization and data analysis activities to be achieved during the tutorial.
After this training session, you will know:
- Install virtual environment con google colab with Miniconda
- Install fundamental packages for simple docking
- Get protein from RSCB and split ligand
- Visualization with py3dmol
- Add hydrogen and gasteiger to protein and ligand
- Conduct molecular docking using smina and quick vina 2
- Advance docking: blind docking, flexible docking and customize scoring functions
- Docking results analysis: indentify interaction and calculate RMSD (redocking)
- Retrospective control analysis (update…)
Description of the Tutorials
The following is a brief description of each tutorial, along with the open-source software used for each task:
| Tutorial | Description | Software |
|---|---|---|
Lab.01  | Install software, ligand and receptor reparation, simple docking | Miniconda, Obabel, py3dmol, RDKit, smina, qvina2, mgltools 1.5.7 |
| Lab.02 | Docking Analysis and advance docking including blind docking, flexible docking and scoring function optimization | Miniconda, Obabel, py3dmol, RDKit, smina, qvina2, mgltools 1.5.7 |