Drug Design Workshop: Molecular Docking with AutoDock (DDW-2022-1)

12 Feb 2022, 09:00 → 13 Feb 2022, 17:00 Asia/Kolkata

A two day workshop on molecular docking with AutoDock. The event comprises lectures and hands-on session covering

• Requirements
• Installation of AutoDock
• Preparation of Protein
• Preparation of Ligands
• Preparation for Molecular Docking
• Execution of Molecular Docking
• Analysis of Molecular Docking

Day 1 Hands-on Session

Day 2 Session 1

Day 2 Session 2

Day 2 Session 3

Presentation (PPT)

Saturday, 12 February

Lecture Session: Session 1

Theoretical background for the hands-on session will be covered during this session

Convener: Prof. Venkatesan Jayaprakash (Birla Institute of Technology, Mesra)

1 Introduction to Structure Based Drug Design (SBDD)

This lecture will cover in-silico virtual screening in general and with Structure Bases Drug Design. How this is helpful in Drug Discovery Development Pipeline?

Speaker: Prof. Venkatesan Jayaprakash (Birla Institute of Technology, Mesra)

2 Lecture by Dr. Murugesan Sankaran

A case study

Speaker: Murugesan Sankaran (Birla Institute of Technology and Sciences, Pilani)

11:00 Tea Break

3 Where and how to start?

This lecture is designed to provide information on how to get start with practicing of molecular docking. Hardware and Software requirements, list of websites useful for the preparation for docking and a general molecular docking protocol.

Speaker: Prof. Venkatesan Jayaprakash (Birla Institute of Technology, Mesra)

Hands-on Session: Hands-on Session 1

Preparation for molecular docking simulation and working with AutoDock4 will be covered during this session.

Convener: Prof. Venkatesan Jayaprakash (Birla Institute of Technology, Mesra)

4 Hands-on Session 1

Protein Preparation
Ligand Preparation
Docking Preparation

Speaker: Prof. Venkatesan Jayaprakash (Birla Institute of Technology, Mesra)

Sunday, 13 February

Lecture Session: Session 3

Theoretical background for the hands-on session will be covered during this session

5 Lecture by Dr. Senthilraja A

A case study

Speaker: Senthilraja A (Indian Institute of Technology (BHU), Varanasi)

Group Discussion: Discussion Session 1

This session will allow participants to discuss with the course coordinators and amongst themselves.

Convener: Prof. Venkatesan Jayaprakash (Birla Institute of Technology, Mesra)

6 Discussion Session

Speaker: Prof. Venkatesan Jayaprakash (Birla Institute of Technology, Mesra)

Hands-on Session: Hands-on Session 2

Preparation for molecular docking simulation and working with AutoDock4 will be covered during this session.

7 Hands-on Session 2

Running AutoDock
Analysis of Docking Results

Speaker: Prof. Venkatesan Jayaprakash (Birla Institute of Technology, Mesra)

Hands-on Session: Hands-on Session 3

Preparation for molecular docking simulation and working with AutoDock4 will be covered during this session.

Convener: Prof. Venkatesan Jayaprakash (Birla Institute of Technology, Mesra)

8 Hands-on Session 3

Preparing complex for further analysis (UCSF Chimera)
Generting 2D-interaction plots using LigPlot+

Speaker: Prof. Venkatesan Jayaprakash (Birla Institute of Technology, Mesra)

Group Discussion: Discussion Session 2

This session will allow participants to discuss with the course coordinators and amongst themselves.

Convener: Prof. Venkatesan Jayaprakash (Birla Institute of Technology, Mesra)

9 Discussion Session 2

Speaker: Prof. Venkatesan Jayaprakash (Birla Institute of Technology, Mesra)