| Attribute | Detail |
|---|---|
| Format | Recorded Lectures |
| Level | Intermediate |
| Duration | 3 Days (60-90 minutes) |
| Certification | e-Certification + e-Marksheet |
| Fee | Free |
| Tools | GROMACS CHARMM-GUI WebGRO MDWeb Google Sheets Excel VMD PyMOL ChatGPT Gemini |
About the Hands-on Molecular Dynamics Simulation, Protein Stability and Binding Free Energy Analysis for Computational Drug Discovery Course
This advanced 3‑day hands‑on program introduces practical concepts of molecular dynamics (MD) simulation, protein‑ligand stability analysis, trajectory interpretation, and binding free‑energy calculations for computational drug discovery.
Move beyond static docking to evaluate how complexes behave over time under realistic biological conditions.
Program Highlights
• Comprehensive coverage of Hands from fundamentals to advanced applications
• Hands-on projects and real-world case studies in Biotechnology
• Expert-curated curriculum aligned with current industry standards
• Access to recorded lectures and e-LMS platform for flexible, self-paced learning
• e-Certification and e-Marksheet upon successful completion
• Dedicated mentor support and interactive doubt-clearing sessions
• Practical experience with tools: GROMACS, CHARMM-GUI, WebGRO, MDWeb
• Career-oriented training for academic and professional growth in Biotechnology
Course Curriculum
Module 1: Day 1 – Introduction to Molecular Dynamics Simulation and System Preparation
- Explain limitations of docking and need for MD validation
- Prepare protein‑ligand complexes for MD (solvation, ions, minimization)
- Run equilibration (NVT/NPT) and production workflows using GROMACS
Module 2: Day 2 – Protein‑Ligand Stability Analysis: RMSD, RMSF & Radius of Gyration
- Interpret RMSD for backbone and ligand to assess stability
- Analyze RMSF to pinpoint flexible residues
- Evaluate radius of gyration for protein compactness
Module 3: Day 3 – Hydrogen‑Bond Analysis, Binding Free Energy & Report Writing
- Quantify hydrogen‑bond persistence and contact stability
- Calculate MM/PBSA or MM/GBSA binding free energies
- Draft research‑style MD reports using AI‑assisted tools
Tools, Techniques, or Platforms Covered
GROMACS CHARMM-GUI WebGRO MDWeb Google Sheets Excel VMD PyMOL ChatGPT Gemini
Real-World Applications
- Apply Hands skills directly to academic research, thesis work, and publications
- Build a professional portfolio showcasing practical Biotechnology competencies
- Solve industry-relevant problems using Hands methodologies and tools
- Contribute to open-source projects and collaborative research in Biotechnology
- Prepare for competitive examinations, interviews, and professional certifications in Biotechnology
Who Should Attend & Prerequisites
- Industry‑recognized e‑Certification + e‑Marksheet from NSTC
- Hands‑on training with real‑world protein‑ligand datasets
- Dedicated expert mentorship and doubt resolution
Certification
