About the Workshop

This 10-Day Online Hands-On Workshop delivers a comprehensive and immersive journey into Computational Drug Design, Molecular Docking, and Molecular Dynamics (MD) Simulation, equipping participants with both theoretical foundations and practical expertise essential for modern drug discovery. The program spans the complete computational workflow—from target identification, ligand preparation, and docking strategies to MD simulation, trajectory analysis, and binding free energy calculations—using widely adopted tools in pharmaceutical and biotech research. Designed for students, academic researchers, and professionals in bioinformatics, biotechnology, pharmacy, chemistry, and life sciences, this workshop empowers participants to independently perform docking studies, validate molecular interactions, run MD simulations, and generate publication-ready results using real biological datasets. Whether you are a beginner or transitioning into computational drug design, this training provides a robust platform to build confidence, sharpen skills, and advance your career in the field of computer-aided drug discovery.

👥 Who Should Attend?

Designed for students, academic researchers, and professionals in bioinformatics, biotechnology, pharmacy, chemistry, and life sciences. Whether you are a beginner or transitioning into computational drug design, this training provides a robust platform to build confidence, sharpen skills, and advance your career in computer-aided drug discovery.

Complete Course Curriculum

Module 1: Foundations of CADD & Pre-processing (Days 1-3)
Day 1: Introduction to In Silico Drug Discovery
08 Dec (Mon)
  • The Drug Discovery Pipeline: Overview of pharmaceutical timeline and computational drug design
  • Ligand-based vs. Structure-based drug design approaches
  • Database Navigation: PDB, PubChem, ChEMBL, ZINC, UniProt
  • Retrieving protein structures and small molecules
Day 2: Protein Structure Preparation & Active Site Analysis
09 Dec (Tue)
  • Structure cleaning: removing water, ligands, and heteroatoms
  • Refinement: fixing missing residues and protonation states
  • Hands-on with UCSF Chimera, PyMOL, Discovery Studio Visualizer
  • Active site prediction using CASTp and PrankWeb
Day 3: Ligand Design, Optimization & ADMET Profiling
10 Dec (Wed)
  • Ligand selection and retrieval from databases
  • Structure drawing with ChemSketch
  • ADMET Analysis: Drug-Likeness (Lipinski's Rule of 5) and toxicity prediction
  • Using SwissADME and pkCSM for filtering ligands
  • File format conversion with OpenBabel
Module 2: Molecular Docking & Interaction Analysis (Days 4-6)
Day 4: Molecular Docking Theory & Setup
11 Dec (Thu)
  • Search algorithms: Genetic Algorithms, Lamarckian GA
  • Scoring functions fundamentals
  • Docking strategies: Rigid vs. Flexible vs. Blind docking
  • Grid box generation and active site definition
  • Input preparation with AutoDock Tools (ADT)
Day 5: High-Throughput Docking Execution
12 Dec (Fri)
  • Working with AutoDock Vina
  • Running docking on single ligands and compound libraries
  • Data handling and organizing output logs
  • Managing multiple poses effectively
Day 6: Post-Docking Analysis & Visualization
13 Dec (Sat)
  • Interpreting binding affinity (kcal/mol) and RMSD values
  • 2D/3D visualization with LigPlot+ and Discovery Studio
  • Interaction profiling: H-bonds, hydrophobic interactions, pi-stacking, salt bridges
  • Generating publication-ready figures
Module 3: Molecular Dynamics Simulation (Days 7-9)
Day 7: MD Simulation Fundamentals & System Setup
14 Dec (Sun)
  • Theory: Newton's laws, force fields (AMBER/CHARMM), water models
  • Introduction to GROMACS in Linux environment
  • Topology generation for proteins and ligands
  • Building protein-ligand complexes
Day 8: Running the Simulation Workflow
15 Dec (Mon)
  • Solvation and neutralization with water box and counter-ions
  • Energy minimization using steepest descent
  • NVT equilibration: temperature stabilization
  • NPT equilibration: pressure stabilization
  • Production run execution
Day 9: Trajectory Analysis & Free Energy Calculation
16 Dec (Tue)
  • Calculating RMSD and RMSF for stability assessment
  • Radius of Gyration (Rg) for compactness analysis
  • Solvent Accessible Surface Area (SASA) calculations
  • Hydrogen bond monitoring over time
Module 4: Capstone & Future Directions (Day 10)
Day 10: Capstone Project & Future Trends
17 Dec (Wed)
  • Capstone project: Complete protein-ligand docking and MD analysis
  • Scientific report formatting and compilation
  • Future trends: AI/Machine Learning in drug discovery (AlphaFold, DeepDocking)
  • Cloud computing in computational chemistry
  • Q&A session and troubleshooting

Who Should Attend

✓ Faculty members teaching computational chemistry or quantum chemistry
✓ Researchers working in computational chemistry and molecular modeling
✓ Graduate and undergraduate students new to computational tools
✓ PhD scholars requiring molecular simulations for their research
✓ Anyone interested in learning computational chemistry and drug design

Learning Outcomes

✓ Understand the fundamentals of Computational Drug Design
✓ Master molecular docking techniques with AutoDock Vina
✓ Perform protein structure preparation and active site analysis
✓ Calculate and analyze ligand-protein interactions
✓ Conduct molecular dynamics simulations using GROMACS
✓ Analyze MD trajectories and calculate binding free energies
✓ Generate publication-ready molecular visualizations
✓ Complete hands-on projects with real molecular systems