Five Day Workshop on Biomolecular Simulations & Drug Discovery
Organiser: Centre for Computational and Integrative Sciences (CCIS),
SRM University - AP (CCIS-2024)
January 29 - February 02, 2024
Overview of the Workshop
Understanding complex biological systems like DNA, RNA, proteins are of utmost importance due to its applications in various real-life scenarios. These systems are in general complex in nature due to the large time scale and length scale involved in various phenomena. The molecular dynamics simulation is one of the widely used method in understanding such systems at the microscopic level. Over the course of five days, we will teach basic details of molecular dynamics, biased sampling simulations such as umbrella sampling and metadynamics and hands-on sessions. Participants will not only grasp theoretical foundations but also apply their knowledge in practical scenarios, making this workshop an invaluable opportunity for anyone keen on advancing their skills in the dynamic field of Molecular Dynamics simulations.
Topics to be Covered
Introductory Module 1
(2 hrs Lecture, 4 hrs hands on)
- 1. Introduction to Molecular Dynamics
- 2. Usefulness of molecular simulations
- 3. Modelling biomolecules
- 4. Available MD simulation tools
- 5. Working environment
- 6. Simple molecular dynamics simulation
Module 2
(2 hrs Lecture, 4 hrs hands on)
- 1. Water model
- 2. Interaction terms
- 3. Force field integrator
- 4. Periodic Boundary conditions
- 5. System building
- 6. Equilibration and production
- 7. Visualization using VMD
Module 3
(2 hrs Lecture, 4 hrs hands on)
- 1. Basics of molecular docking
- 2. Rigid and flexible docking
- 3. Blind docking
- 4. Available tools
- 5. Docking simulation
- 6. Interpretation of results
Module 4
(2 hrs Lecture, 4 hrs hands on)
- 1. Systems with rare events
- 2. Difficulty in using unbiased simulation.
- 3. Introduction to enhanced sampling
- 4. Available biased techniques
- 5. Umbrella sampling
- 6. Simulation using umbrella sampling.
Module 5
(2 hrs Lecture, 4 hrs hands on)
- 1. Introduction to Metadynamics
- 2. Comparison with Umbrella Sampling
- 3. Well-tempered metadynamics
- 4. Ligand – protein system
- 5. Metadynamics simulation
- 6. Analyse hills file Free Energy calculations
- 7. Segregating efficient drug from a list of compounds
Tutors
Dr Atanu Kumar Metya
Email ID:
atanu.metya[AT]iitp.ac.in
Dr Debabrata Pramanik
Email ID:
debabrata.p@srmap.edu.in
Dr Naga Bhushana Rao Karampudi
Email ID:
nagabhushan.k@srmap.edu.in
Important Dates
| Dates of the workshop | January 29 - February 02, 2024 |
| Last date for Registration | January 15, 2024 |
Contact Us
Dr Debabrata PramanikEmail ID: debabrata.p@srmap.edu.in
Dr Mahesh Kumar RavvaEmail ID: mahesh.r@srmap.edu.in
Organising Committee
Convener
- Dr Mahesh Kumar Ravva, SRM University-AP, Andhra Pradesh
- Dr Debabrata Pramanik, SRM University-AP, Andhra Pradesh
Registration
For Registration - http://surl.li/opozk
(Committee will inform the selected participants)
| Category | Online |
| Students/Post-docs from India | INR 500 |
| Scientists/Faculty Members | INR 1000 |
| Industry Personnel | INR 2500 |