One-Day Hands-On Workshop on Molecular Modelling: Building and Simulating Biomolecules

 

The Department of Biotechnology, School of Applied and Life Sciences, successfully conducted a one-day hands-on workshop titled “Hands-On Molecular Modelling Workshop: Building and Simulating Biomolecules” on 24th November 2025 in the Bioinformatics Laboratory. The workshop was expertly led by Dr. Jerin James, Assistant Professor, Department of Biotechnology, who possesses rich experience in computational structural biology, molecular docking, and dynamics simulations. 

A total of 48 participants—including B.Sc. Biotechnology, and M.Sc. Biotechnology students, along with a few Ph.D. scholars—enthusiastically attended the programme. The primary objective was to impart practical, industry-relevant skills in computational tools essential for modern drug discovery and structural bioinformatics. 

The workshop was divided into morning and afternoon sessions packed with intensive hands-on training. The morning session focused on retrieving protein and DNA structures from the Protein Data Bank (PDB), 3D visualization, structural analysis, and editing using PyMOL and UCSF Chimera, as well as constructing small organic molecules and peptides using Avogadro software. In the afternoon session, participants were introduced to molecular docking concepts and applications; they performed step-by-step protein-ligand docking experiments using AutoDock Vina, analyzed binding poses, docking scores, and intermolecular interactions, and gained exposure to energy minimization techniques. The session concluded with an overview of the molecular dynamics simulation workflow using GROMACS, trajectory analysis using VMD, and interpretation of simulation results. 

Every participant worked independently on provided datasets and successfully generated docking results while visualizing the dynamic behavior of biomolecules. Ready-to-use protocols and command scripts were shared for future reference. The completely practical-oriented format, lucid explanations by Dr. Jerin James, and immediate doubt-clearing made the learning highly effective. Participants highlighted the direct relevance of the acquired skills for their academic projects, research work, and future careers in computational biology and drug design. Many requested advanced-level follow-up workshops on full-length GROMACS simulations and virtual screening.