Molecular Dynamics of Protein–Ligand Interactions | NSTC
Molecular Dynamics Simulation of Protein Stability and Protein–Ligand Interactions is an intermediate-level, 6-week online internship by NSTC.
- ModeOnline, Live + LMS
- LevelBeginner
- Fee₹5,499
| 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.
