| Attribute | Detail |
|---|---|
| Format | Online, Live + LMS |
| Level | Beginner |
| Certification | e-Certification + e-Marksheet |
| Fee | ₹5499 / $99 |
| Tools | Select a therapeutic target and retrieve a suitable protein structure. Clean the protein, prepare the ligand, and generate the molecular complex. Select a force field and generate topology and parameter files. Create the simulation box, solvate the system, add ions, and minimise energy. Conduct NVT and NPT equilibration followed by production simulation. Analyse stability, flexibility, interactions, and binding-energy behaviour. GROMACS Google Colab GROMACS Workflows VMD PyMOL ChimeraX MDAnalysis MDTraj Python AutoDock Vina Protein Data Bank Prepared protein or protein–ligand molecular system Topology, parameter, and simulation-input files Processed molecular dynamics trajectory RMSD, RMSF, radius of gyration, and SASA plots Hydrogen-bond, interaction-map, and binding-energy analysis Publication-quality figures, scientific report, and final presentation Molecular Dynamics Investigation of a Cancer Drug–Target Complex Protein Stability Analysis of Disease-Associated Mutations Molecular Dynamics Validation of Molecular Docking Results Comparative Simulation of Wild-Type and Mutant Enzymes Binding Stability of Natural Compounds Against Viral Proteins Molecular Dynamics Study of Protein–Protein Interactions |
About the Molecular Dynamics of Protein–Ligand Interactions | NSTC Course
Attribute
Detail
Format
Online, Live + LMS
Level
Intermediate
Recommended Duration
2–6 Weeks
Certification
e-Certification + e-Marksheet
Category
Computational Biology and Drug Discovery Internship
Tools
GROMACS, VMD, PyMOL, ChimeraX, MDAnalysis, MDTraj, Python, AutoDock Vina, and Google Colab
The Molecular Dynamics Simulation of Protein Stability and Protein–Ligand Interactions Internship is a project-based programme designed to introduce participants to the complete molecular dynamics simulation workflow used in structural biology, bioinformatics, and computational drug discovery.
Participants will retrieve and prepare protein structures, generate protein–ligand complexes, select force fields, create simulation boxes, solvate systems, add ions, perform energy minimisation, conduct equilibration, and run production molecular dynamics simulations.
The resulting trajectories will be analysed through RMSD, RMSF, radius of gyration, solvent-accessible surface area, hydrogen bonding, protein–ligand contact analysis, free-energy landscapes, and binding-energy estimation where supported.
Aim
To prepare, simulate, and analyse protein or protein–ligand systems for evaluating structural stability, conformational flexibility, molecular interactions, and binding behaviour.
Program Highlights
• Protein and protein–ligand system preparation
• GROMACS-based molecular dynamics workflows
• Energy minimisation and system equilibration
• Structural stability and flexibility analysis
• Protein–ligand interaction and contact analysis
• Scientific reporting and publication-quality plots
Course Curriculum
- Structural stability analysis using RMSD and radius of gyration
- Residue-level flexibility analysis using RMSF
- Hydrogen-bond and solvent-accessible surface-area analysis
- Protein–ligand contact and binding-pocket stability analysis
- Free-energy landscape and conformational-state analysis
- MM/PBSA-style binding-energy estimation where supported
Week 1: Target and Structure Preparation
- Select a therapeutic protein target.
- Retrieve and inspect the three-dimensional structure.
- Clean the protein and remove unnecessary molecules.
- Prepare the ligand or initial protein complex.
- Inspect the binding site and important residues.
Week 2: Molecular System Preparation
- Select an appropriate force field and water model.
- Generate protein and ligand topology files.
- Define the simulation box and periodic boundaries.
- Solvate the system and add counterions.
- Perform energy minimisation and inspect convergence.
Week 3: System Equilibration
- Prepare NVT equilibration input parameters.
- Stabilise the system temperature.
- Conduct NPT equilibration.
- Validate temperature, pressure, density, and energy.
- Confirm system stability before production simulation.
Week 4: Production Molecular Dynamics Simulation
- Prepare the production simulation input file.
- Run the molecular dynamics simulation.
- Monitor simulation progress and computational performance.
- Process and manage trajectory files.
- Document simulation parameters and system conditions.
Week 5: Structural Stability and Interaction Analysis
- Calculate RMSD, RMSF, and radius of gyration.
- Analyse solvent-accessible surface area.
- Evaluate hydrogen bonds and secondary-structure changes.
- Examine protein–ligand contacts and pocket stability.
- Compare structural behaviour across simulation systems.
Week 6: Energy Analysis and Final Reporting
- Generate free-energy landscape plots.
- Estimate binding energy where supported.
- Prepare publication-quality figures and interaction maps.
- Complete the scientific report and discuss limitations.
- Present the final project and attend the technical viva.
Tools, Techniques, or Platforms Covered
- Select a therapeutic target and retrieve a suitable protein structure.
- Clean the protein, prepare the ligand, and generate the molecular complex.
- Select a force field and generate topology and parameter files.
- Create the simulation box, solvate the system, add ions, and minimise energy.
- Conduct NVT and NPT equilibration followed by production simulation.
- Analyse stability, flexibility, interactions, and binding-energy behaviour.
GROMACS Google Colab GROMACS Workflows VMD PyMOL ChimeraX MDAnalysis MDTraj Python AutoDock Vina Protein Data Bank
- Prepared protein or protein–ligand molecular system
- Topology, parameter, and simulation-input files
- Processed molecular dynamics trajectory
- RMSD, RMSF, radius of gyration, and SASA plots
- Hydrogen-bond, interaction-map, and binding-energy analysis
- Publication-quality figures, scientific report, and final presentation
Molecular Dynamics Investigation of a Cancer Drug–Target Complex
Protein Stability Analysis of Disease-Associated Mutations
Molecular Dynamics Validation of Molecular Docking Results
Comparative Simulation of Wild-Type and Mutant Enzymes
Binding Stability of Natural Compounds Against Viral Proteins
Molecular Dynamics Study of Protein–Protein Interactions
Real-World Applications
- Validation of protein–ligand docking results
- Assessment of protein stability and disease-associated mutations
- Evaluation of drug-binding stability and molecular interactions
- Comparison of wild-type and mutant protein structures
- Investigation of viral, cancer, and enzyme therapeutic targets
- Support for computational drug discovery and structural biology research
Who Should Attend & Prerequisites
- Biotechnology, bioinformatics, and computational biology students
- Biochemistry, molecular biology, and pharmaceutical science learners
- Undergraduate and postgraduate students
- PhD scholars and early-career researchers
- Drug-discovery and structural-biology professionals
- Learners interested in molecular modelling and simulation
Outcomes
- Protein-structure cleaning and missing-atom inspection
- Force-field selection and topology generation
- Simulation-box preparation, solvation, and ion addition
- Energy minimisation and NVT/NPT equilibration
- Trajectory processing and structural-stability analysis
- Scientific visualisation and simulation-result interpretation
Certification
