Two-Day Molecular Docking Workshop
Join our two-day hands-on workshop and dive into the world of computational drug design. Learn to prepare proteins and ligands, run docking simulations with AutoDock Vina, and visualize binding interactions using PyMOL/Chimera. Perfect for students and researchers, this workshop equips you with practical skills to explore molecular interactions and accelerate drug discovery.
Gain hands-on experience in computational drug discovery using AutoDock Vina, PyMOL, and Chimera. Learn to prepare proteins and ligands, run docking simulations, and analyze binding interactions through practical sessions and case studies.
đź“… Date: 20 & 21 September 2025
Day 1 – Fundamentals & Preparation
Session 1: Introduction & Basics
- Principles and applications of molecular docking
- AutoDock Vina features & workflow
- Installing required tools (AutoDock Vina, ADT, PyMOL/Chimera)
Session 2: Protein & Ligand Preparation
- Protein retrieval (PDB) from RCSB
- Cleaning protein: removing water, adding hydrogens, fixing missing atoms
- Ligand preparation: PubChem/ChemSpider download, energy minimization, PDBQT conversion
- File format conversions (PDB → PDBQT)
Hands-on Exercise: Prepare a protein and a ligand for docking.
Day 2 – Docking & Analysis
Session 3: Docking Run
- Defining active/binding sites
- Grid box generation in AutoDock Tools
- Running docking simulations (command line)
Hands-on Exercise: Perform docking, analyze best pose, and visualize binding interactions.
Session 4: Results & Visualization
- Interpreting docking outputs (binding affinity, poses, log files)
- Visualizing docking interactions (PyMOL/Chimera/Discovery Studio)
- Case study: Ligand docking into a selected protein target
Dr. Vikas Kumar
Dr. Vikas Kumar is currently working as an Associate Professor in the Department of Biotechnology at Chandigarh University, Gharuan, Mohali, Punjab, India. He earned his PhD in Biotechnology from Shoolini University, Solan, Himachal Pradesh, India. His research involves the association of genetic diversity and phytochemical variations of Terminalia arjuna tree from North-Western Himalayas. Dr. Kumar also holds an MSc in Biotechnology and a BSc in Medical. He qualified for the ARS-NET in Agricultural Biotechnology in 2014 and has 10 years of teaching experience at the university level.
To date, Dr. Kumar has published 11 review articles, 50 research articles, and 5 book chapters in prestigious publishers like Elsevier, Springer, Taylor and Francis, and MDPI. He is a regular reviewer for MDPI journals and an AdHoc reviewer for Springer and Elsevier journals. He has also participated in several national and international conferences, delivering two oral presentations that helped him mature as a researcher. Dr. Kumar was awarded the best poster award at the international conference “Science Emerging Scenario and Future Challenges,” organized by the Him Science Congress Association at the National Institute of Technology, Hamirpur, Himachal Pradesh, India, in 2018.