Molecular Modeling & MD Simulations: Cohort Bootcamp
Become the student who can actually run the simulations, not just read about them.
A live, mentor-led cohort on molecular modelling, docking and molecular dynamics of proteins, from finding a structure to running your own MD simulation and computing binding free energy, finishing with a project you build yourself and can show on your CV, SOP, and graduate-school applications.
Reserve your seatThis cohort takes you through the full computational workflow for proteins, protein databases, homology modelling, molecular docking, molecular dynamics in GROMACS, and binding free energy, hands-on, in a small live group capped at 10 students. You finish with a complete docking + MD project you build end to end and can demonstrate.
The details
What you’ll be able to do
- Find, model and validate a 3D protein structure using databases and homology modelling (AlphaFold).
- Dock a drug molecule into a protein and analyse the interaction with AutoDock and LigPLOT.
- Build and run a molecular dynamics simulation in GROMACS, from setup to a finished trajectory.
- Analyse trajectories (RMSD, RMSF) with Python and compute binding free energy, and present it the way a researcher does.
- Finish a working capstone project you can demo on your CV, SOP, and applications.
What you’ll work through
Protein structures & databases
Find and read protein structures in the PDB, RCSB and UniProt, chains, residues, ligands, resolution, and what a binding site looks like.
Homology modelling & structure prediction
Build a 3D model when no experimental structure exists, predict structure with AlphaFold, then refine and validate the model.
Molecular docking
Prepare a protein and ligand, run docking in AutoDock, and interpret binding poses and affinity scores, the right way, avoiding the mistakes that wreck results.
Drug–protein interaction analysis
Map the contacts that drive binding with LigPLOT and explain why a molecule binds the way it does.
Molecular dynamics in GROMACS
Build the system, solvate, energy-minimise, equilibrate (NVT/NPT) and run a real MD simulation, understanding what every stage is for.
Trajectory analysis & binding free energy
Analyse the trajectory with Python, VMD and Xmgrace (RMSD, RMSF, hydrogen bonds), compute binding free energy, and finish your capstone project.
Why a live cohort beats video courses
Live, not pre-recorded
You work through the tools with a mentor in real time on Google Meet, not another folder of recordings you never finish.
Hands-on from the start
You run the real software on a real system from the first sessions. Skill comes from doing.
Feedback on your work
A mentor reviews your project and unblocks you, so you do not lose days stuck on a setup error.
A group of 10
Seats are capped at 10, so you are a participant getting direct time, not one of thousands watching a screen.
Is this for you?
✓ This is for you if…
- You are a BSc or MSc student in life sciences, chemistry, or a related field
- You are aiming at research, a thesis, or graduate school
- You want practical computational skills your syllabus skips, plus proof you have them
✗ It is not for you if…
- You only want to watch videos passively
- You are not willing to do hands-on work between sessions
- You want a certificate without the skill behind it
Who is teaching it
You learn from working scientists with more than a decade of hands-on experience in sequence and structural bioinformatics, drug discovery and design, and multiscale molecular modelling, using the same computational techniques you will be taught. The cohort is kept small so every student gets direct mentor time and feedback on their own project.
Our mentors publish the methods they teach
Together, the StemSkills team has authored 70+ peer-reviewed papers · cited 1,390+ times · across 38 journals, work in molecular docking, molecular dynamics and structure prediction, in journals like Bioinformatics and Scientific Reports. You learn these methods from the people who use them in real research.
What it costs
International learners: $200 · + 18% GST
Seats are limited to 10 and the cohort starts 6 July 2026. Reserve your seat below and we’ll confirm your spot and the payment details.
- Live, mentor-led sessions
- Hands-on labs every week
- Direct feedback on your project
- Your own working capstone project
- Certificate of completion
- Small group, capped at 10
Reserve your seat
Seats are limited to 10 and confirmed in order. Fill in the registration form and we’ll confirm your spot and share the payment details.
Open the registration form →Questions students ask
Do I need to know how to code?
No. The cohort is built for students new to computational tools. You start from setup and build up, with a mentor. You will pick up the Python you need for trajectory analysis along the way.
What will I actually build?
A working project of your own: you model and validate a structure, dock a molecule, run a molecular dynamics simulation, analyse it and compute binding free energy, a project you can demonstrate.
How much time each week?
Two live sessions a week of 1–1.5 hours each, over about two months, plus practice between them.
What does it cost?
₹10,000 for students in India and $200 internationally, plus 18% GST.
What do I need to take part?
A laptop with Ubuntu installed. We help you set it up before the cohort starts. Sessions run live on Google Meet.
When does it start?
6 July 2026 at 6 PM IST. Seats are capped at 10 and confirmed in order, so reserve early.
10 seats · starts 6 July 2026 · live on Google Meet.