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Molecular Dynamics of Protein–Ligand Interactions | NSTC
Original price was: INR ₹149.00.INR ₹99.00Current price is: INR ₹99.00.
Molecular Dynamics Simulation of Protein Stability and Protein–Ligand Interactions is an intermediate-level, 6-week online internship by NSTC. Learn molecular-system preparation, MD simulation, trajectory analysis, protein stability evaluation, and binding-interaction interpretation through practical projects, real datasets, and expert mentorship. Earn an e-Certificate and e-Marksheet upon successful completion.
Internship Details
About the Internship
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.
Internship Objective
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
Simulation Analyses Covered
- 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
Hands-on Activities
- 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.
Core Molecular Dynamics Skills
- 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
Internship Curriculum
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 and Platforms Covered
GROMACS
Google Colab GROMACS Workflows
VMD
PyMOL
ChimeraX
MDAnalysis
MDTraj
Python
AutoDock Vina
Protein Data Bank
Final Deliverables
- 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
Suggested Project Titles
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
Prerequisites: Basic knowledge of protein structure, molecular interactions, and bioinformatics is recommended. Familiarity with Linux commands, molecular docking, or Python is helpful but not mandatory.
Frequently Asked Questions
1. What is this molecular dynamics internship about?
The internship focuses on preparing, simulating, and analysing protein and protein–ligand systems to evaluate stability, flexibility, intermolecular interactions, and binding behaviour.
2. Is this internship suitable for beginners?
The internship is most suitable for intermediate learners, although guided workflows are provided for participants with basic knowledge of protein structure and bioinformatics.
3. Will participants run an actual molecular dynamics simulation?
Yes. Participants will prepare a molecular system, perform minimisation and equilibration, run a production simulation, and analyse the resulting trajectory.
4. Is molecular docking included?
AutoDock Vina may be used for initial protein–ligand complex preparation, while the primary focus remains molecular dynamics simulation and trajectory analysis.
5. Which analyses will be performed?
Participants will perform RMSD, RMSF, radius of gyration, SASA, hydrogen-bond, interaction-contact, free-energy landscape, and binding-energy analyses where supported.
6. What will participants submit after completion?
Participants will submit the prepared simulation system, input and topology files, trajectory results, analysis plots, interaction maps, binding-energy summary, scientific report, and final presentation.
The Molecular Dynamics Simulation of Protein Stability and Protein–Ligand Interactions Internship provides practical experience in molecular-system preparation, GROMACS simulation, trajectory processing, structural-stability analysis, protein–ligand interaction assessment, and scientific reporting. Participants will complete a structured computational project relevant to structural biology, bioinformatics, pharmaceutical research, and computer-aided drug discovery.
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