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 Free Online Multi-Ligand Docking using Autodock Vina

3 Hours long Workshop
Dates: September 11, 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.  

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WhatsApp Group Link:
Join here for Free Workshop

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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.

 

Certificate WhatsApp Group Link:
Join here for Certificate, recording and tutorial

 

Agenda:

1. Introduction to Multi-Ligand Docking

  • 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.

  • Sorting ligands based on their binding affinity and energy scores.

  • Selecting the top candidates for further analysis.

8. Visualizing Binding Modes:

  • Using Maestro or Online tools to visualize the ligand-receptor interactions.

  • Identifying key interactions (hydrogen bonds, hydrophobic interactions, pi-pi stacking, etc.).

  • Comparing interactions between multiple ligands and the receptor to select the best leads.

  • Docking Validation (Optional)

9. Redocking and RMSD Validation:

  • Performing re-docking with the native ligand to validate the docking protocol.

  • Superimposing the docked poses with the native ligand to check RMSD values.

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