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 Free Online Molecular Docking Hands-on Workshop using AutoDock 4

2 Hours long Workshop
Dates: September 22, 2024
Time: 7:00 PM - 9:00 PM IST

All participants are requested to join the WhatsApp group, as the session 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:


Join here for Free Workshop

 

*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 Molecular Docking:
•    Overview of the Drug Discovery Pipeline.
•    Introduction to Molecular Docking and Key Concepts.

2. 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. Ligand preparation:
•    Ligand preparation using AutoDockTool
•    Adding polar hydrogen, charges and converting to pdbqt format.

4. Defining Active site for Docking (Grid parameter file generation):
•    Defining the receptor and ligand for grid parameter file generation.
•    Extracting coordinates to define the grid box center.
•    Generating the final grid parameter file.

5. Running the Docking:
•    Selecting the docking algorithm and generating the final docking parameter file.
•    Executing the final docking run.

6. Docking Results Overview:
•    Reviewing docking scores (binding affinities) for ligand.
•    Extracting and analyzing the best binding modes and docking scores from the output files.

7. 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.).

8. Docking Validation:
•    Superimposing docked poses with the native ligand to check RMSD values
•    Ensuring accurate docking results through validation

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Registration Fees with Certificates

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Indian Participants- 200 INR 

Foreign Nationals-5 USD

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