Half day Pilot Workshop on AutoDock4 on 09 August 2024

Introduction

AutoDock4 is a widely-used open source software suite for molecular modeling, specifically for predicting how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Developed by the Scripps Research Institute, it combines two primary components: AutoDock and AutoGrid.

AutoDock4 is used for molecular docking and virtual screening, particularly in the field of drug discovery and computational chemistry. 

AutoDockTools is an interactive graphical tool for coordinate preparation, docking and analysis for the AutoDock suite. 

Here are the key benefits of using AutoDock4:

1. Accurate and Reliable Docking

2. Flexible Receptor and Ligand Docking

3. Comprehensive Search Algorithms

4. Customizability of parameters of the docking process, allowing for tailored simulations

5. Integration with Visualization Tools such as PyMOL and VMD,

6. Open Source and Free software, making it accessible to researchers worldwide without the need for expensive licenses.

7. Large User Community and Extensive Documentation

8. Support for Virtual Screening

9. Cross-Platform Compatibility. The software runs on Windows, macOS, and Linux

10. Automated Workflow Integration

AutoDock4 is a powerful tool for researchers in computational biology, chemistry, and drug design, providing insights into molecular interactions that are crucial for drug development and other scientific inquiries.

During the workshop, we will cover installation and basic features of AutoDock4 . By the end of it, participants will have a good understanding of docking of small molecules to macromolecular receptors and analyzing docking runs.

The Spoken Tutorial project at IIT Bombay (https://spoken-tutorial.org/) was established by Ministry of Education, Govt. of India.

Methodology of the Workshop

The workshop will be conducted using pre-recorded spoken tutorial videos with side by side learning. For a comprehensive understanding of each topic, practice problems will be provided following each tutorial.

All participants will receive the Spoken Tutorials on AutoDock4, along with the slides and the code files used in the tutorial.

Benefits of the Workshop

On successful completion of the workshop, participants will 

• Learn to use AutoDock4 program for docking small molecules to receptors and analyze the docking runs.

• Get certificate for attending half-day AutoDock 4 pilot workshop.

Course content

At the end of this workshop, participants will be able to:

• Download the required ligand and receptor files from database websites.
• Perform ligand and receptor refinement process so that they can be used by the AutoDock program to perform docking.
• Create a grid for the receptor molecule and run the autogrid program.
• Perform docking using default docking parameters and run AutoDock program.
• Analyze the docking runs.
• Visualize the docking process using open source visualization software.

Teaching Faculty

• Prof. Kannan Moudgalya, Faculty, Chemical Engineering, IIT Bombay
• Ms. Sruthi Sudhakar, PhD student, Department of Chemistry IIT Bombay, ( Domain expert on AutoDock4)
• Spoken Tutorial Team IIT Bombay

Who Should Attend

The AutoDock workshop will be useful for:

• Biochemists and Molecular Biologists
• Drug Discovery Researchers
• Academic Researchers
• Computational Chemists
• Structural Biologists
• Medicinal Chemists
• Bioinformaticians
• Biotechnology companies

Duration and Venue

Half-day Pilot Workshop on AutoDock4 will be online on 9 August 2024 from 2.00 pm to 5.30 pm. 

Criteria for Certification

Participation certificates, in an electronic form, will be provided to all participants after successful completion of the workshop.

Course Fee

This Pilot workshop will be free of cost.

How to Apply

The application will be strictly online, and no other mode of application will be entertained. The link for online registration is 

https://www.it.iitb.ac.in/nmeict/workshopContent.html?workshopid=PHWqGSga6xPlgDupzMjZ_Q&category=ryjCPtOBugIe3qrCMGqopQ

The registration form will be available until 08 August 2024, 12.00 noon.

Accommodation

Not Applicable

Note

As the workshop is conducted online, it is mandatory to have a laptop and a working internet connection with good bandwidth.

Technical Requirements: It is mandatory to have 

• AutoDock suite 4.2.6
• AutoDock Tools version 1.5.7 
• UCSF Chimera version 1.17.2 
• Following operating systems can be used for installing the above software:
• Windows: 32/64-bit 10 or newer
• Linux: 32/64-bit x86 Ubuntu 18.04 or newer 
• macOS: 10.7 (OS X Lion) or newer

Prerequisite:

• Basic knowledge of Biochemistry

Contact Us:

Any queries can be asked through eoutreach@cse.iitb.ac.in

Address For Communication

Ms. Priti Ghuikar - Dod
Assistant Project Manager
Department of CSE, Kanwal Rekhi Building,
Indian Institute of Technology Bombay,
Mumbai - 400 076.
Email: eoutreach@cse.iitb.ac.in
Website - www.it.iitb.ac.in/nmeict