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Molecular Dynamics (MD) simulations are crucial for understanding biomolecular interactions. One of the most substantial applications is simulating protein-ligand complexes, which is essential for drug discovery, protein engineering, and structural biology. MD simulations provide a detailed molecular-level perspective of drug binding to proteins, including stability and overall binding process.
This workshop will present a thorough overview of simulating protein-ligand interactions using GROMACS, a leading software tool in the field of computational biology. Participants will receive both theoretical insights and hands-on experience with real-world examples, making this an invaluable opportunity for anybody wishing to use MD simulations in their research or profession.
Upon completion of this training, participants will:
1.Understand the principles of molecular dynamics and the importance of protein-ligand interactions.
2.Gain hands-on expertise with GROMACS to simulate protein-ligand complexes.
3.Learn how to set up protein and ligand structures for MD simulations.
4.Understand how to create force fields, run simulations, and analyse findings to determine binding affinity and stability.
5.Be able to simulate protein-ligand binding to determine the most stable conformations.
6.Know how to evaluate important simulation data such as RMSD (Root Mean Square Deviation), RMSF (Root Mean Square Fluctuation), and energy profiling.
The program will be conducted in interactive sessions, with a focus on practical training with GROMACS to simulate protein-ligand interactions. This methodology includes:
1.Introduction to MD Simulations: An overview of molecular dynamics, force fields, and the significance of simulating protein-ligand interactions.
2.Software Setup: Participants will learn how to set up and operate GROMACS on their computer.
3.Preparing inputs: Practical training on creating protein structures, ligands, and systems for MD simulations, including tools for protein-ligand docking and setup.
4.Simulation Process: Step-by-step instructions for setting up, executing, and troubleshooting MD simulations of protein-ligand complexes with GROMACS.
5.Post-Simulation Analysis: Participants will learn how to analyse simulation findings with software such as VMD (Visual Molecular Dynamics), PyMOL, and other visualisation tools. RMSD, RMSF, and energy estimations are some of the Key outputs which will be explored..
6.Case Study Application: In a practical case study, participants will be able to apply their knowledge to simulate an actual protein-ligand interaction.
The lessons will include a mix of theory, practical demonstrations, and hands-on experience to ensure a balanced approach to learning.
PRACTICAL APPLICATION
DAY 1
DAY 2
DAY 3
DAY 4
DAY 5
This event is ideal for:
1. Students and Early Career Researchers: Anyone wanting to obtain practical experience in molecular simulations, particularly those interested in MD simulations or GROMACS, including students (Bachelor’s, Master’s, PhD, MBBS, MD), as well as faculty members and professors from fields such as Microbiology, Biochemistry, Genetics, Plant Science, and Life Sciences.
2.Drug Discovery Researchers: Experts in drug design and development, with a focus on understanding protein-ligand interaction and stability.
3.Structural biologists and chemists: Those who research the structural dynamics of proteins and how they interact with tiny molecules.
4.Bioinformaticians and Computational Biologists: People in computational biology who seek to incorporate MD simulations into their research workflows.
After attending this workshop, participants will be able to:
1.Comprehensive skills in MD simulations
- GROMACS-based molecular dynamics simulations can be performed independently.
- Ability to prepare, conduct, and analyse MD simulations for biomolecular systems.
- Confident in troubleshooting frequent errors that arise during MD simulations.
2.Experience with Real-World Applications.
Participants will get practical insights into how MD simulations are used in:
- Structural Biology: Understanding of protein folding, misfolding and conformational changes.
- Biotechnology: Developing biomolecules for industrial and therapeutic uses.
- Genetic research: Involves studying the consequences of genetic changes on molecular structures.
3.Resources & Support
- Students have access to all course resources, including tutorials, guides, and case studies.
- Video records of all sessions are kept for future reference.
- Certificates of participation give significance to your academic or professional profile.
1.Learn from Experts: Our instructors have extensive expertise of MD simulations and practical applications in drug development and structural biology.
2.Interactive sessions: GROMACS, the industry's top molecular dynamics software, provides hands-on training and practical demonstrations.
3.Real-world Applications: Focus on simulating protein-ligand interactions using real-life scenarios from drug discovery and structural biology.
4. Hands-on Support: Direct, interactive learning with experts guiding you through each step of the process.
5.Networking opportunities: Engage with professionals and researchers from across the world, growing your network in the field of bioinformatics and computational biology.
Register Now
Join us for this immersive training event to obtain the skills required to use MD simulations in your study and profession.
Don't miss this opportunity to immerse yourself in the world of Molecular Dynamics Simulations and learn how to simulate protein-ligand interactions with GROMACS. Improve your abilities and stay competitive in the fields of bioinformatics and computational biology!
Resource Person: Sharvari Kulkarni
Event Duration: 5 days
Mode: Online (via Google Meet/Zoom)
Daily Schedule: 1.5-hour interactive sessions
Event Date : 5 - 9 December, 2024
Certificate: Participation Certificate upon successful completion
| Category | Price |
|---|---|
| Participants Outside India | $ 209 US |
| Participants in India | ₹ 3160 |
