Dates: October 14, 2024
Time: 10:00 AM – 1:00 PM IST

*All participants are requested to join the WhatsApp group, as the session’s online link will be shared exclusively through WhatsApp. It is essential to join the group to receive the necessary information for the session.  

WhatsApp Group Link:
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*The workshop is free to attend, but participants who wish to receive a certificate, access video recordings, and tutorial-style materials for the session can opt-in for a nominal fee of Rs. 200 for Indian participants and $5 for international participants. The payment link will be shared in the WhatsApp group linked below, kindly join the group only if you are opting for the certificate, video recordings, and tutorial materials.

• Overview of docking multiple ligands against a single receptor.
• Introduction to AutoDock Vina and its advantages in high-throughput docking.

2. Selecting and Preparing the Target Receptor:

• Downloading the receptor structure from the PDB database.
• Cleaning and preparing the receptor (removing water molecules, adding hydrogens, adding charge, etc.).

3. Converting to. pdbqt format:

• Using AutoDockTools (ADT) to convert the receptor to. pdbqt format.
• Setting up the active site by defining the grid box around the binding site.

4. Creating or Downloading a Virtual Ligand Library:

• Downloading ligands from the ZINC database.
• Ensuring ligands are energy minimized and in the correct format.
• Preparing multiple ligands for docking (converting to .pdbqt using Open Babel).

5. Configuration of Vina Input Files:

• Preparing a configuration file (.conf) for AutoDock Vina specifying the receptor, grid box dimensions, and number of ligands to dock.

6. Running the Docking:

• Executing AutoDock Vina in command line using single ligand.
• Multiple ligands docking using PyRx software.

7. Docking Results Overview:

• Reviewing docking scores (binding affinities) for each ligand.
• Extracting and analyzing the best binding modes and docking scores from the output files.
• Validating docking protocol (RMSD values calculation between Experimental and Docked ligand)

8. ADME/Tox Prediction

•  ADME/Tox prediction using online server (e.g., SwissADME, pkCSM, or ADMETlab)
• Interpretation of the results
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