Van Thinh To

Van Thinh To

Undergratute in Pharmacy; Interest in applying machine learning techniques, cheminformatics and automated pipeline to screen new biologically active molecules.

Molecular Docking Colab

Internal training, University of Medicine and Pharmacy at Ho Chi Minh city, Department of Organic Chemistry, 2023

This is a set of two (4) tutorials on basic information of molecular docking incoporating python framework, using the Google Colab free cloud-computing environment in Summer 2023. You can watch this tutorial to learn how to use Google Colab. Please download the presentation here. Or you can read the Vietnamse document.

thesis slide

Introduction

These tutorials were created between May-June 2023 as part of the MedAI Training Session 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:

TutorialDescriptionSoftware
Lab.01 Open In ColabTheoretical concepts, Install softwareMiniconda, Obabel, py3dmol, RDKit, Autodock vina 1.2.0, vina-gpu, smina, qvina2, mgltools 1.5.7
Lab.02 Open In ColabMolecular docking pipeline, redocking analysis, interactions extractionMiniconda, Obabel, py3dmol, RDKit, Autodock vina 1.2.0, vina-gpu, smina, qvina2, mgltools 1.5.7
Lab.03 Open In ColabPDBfixer for missing residues handlingCondacolab, openmm, pdbfixer, py3dmol, rdkit
Lab.04 Open In ColabAdvanced docking with smina: whole protein docking, flexible docking and reverse dockingMiniconda, Obabel, py3dmol, RDKit, smina, mgltools 1.5.7
Homology Open In ColabAlphafold2Alphafold2