10-Day Computational Drug Design Workshop

About the Workshop

This 10-Day Online 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.

👥 Who Should Attend?

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. Perfect for undergraduate students, graduate researchers, PhD scholars, faculty members, and industry professionals looking to master computational chemistry techniques.

Workshop Registration Fee

UG/PG Student

₹1499 INR

International Participant

$50 USD

PhD Scholar/Researcher

₹1999 INR

Faculty

₹2499 INR

Industry Professional

₹2999 INR

✓ Includes: Recordings • Study Materials • Certificate • Software Support

📚 Complete Course Curriculum

Module 1: Foundations of CADD & Pre-processing (Days 1-3)

Day 1: Introduction to In Silico Drug Discovery

09 January (Friday)

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

10 January (Saturday)

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

11 January (Sunday)

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

12 January (Monday)

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

13 January (Tuesday)

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

14 January (Wednesday)

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

15 January (Thursday)

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

16 January (Friday)

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

17 January (Saturday)

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
MM-PBSA binding free energy calculations

Module 4: Capstone & Future Directions (Day 10)

Day 10: Capstone Project & Future Trends

18 January (Sunday)

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
Certificate distribution and closing remarks

👥 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

📥 Download Workshop Resources

Pre-Workshop Requirements (PDF) Workshop Handout (PDF) Study Materials (ZIP)

✨ What's Included

🎥 Recorded Sessions - Access all workshop recordings anytime

📘 Comprehensive Study Materials - Complete documentation and guides

🛠️ Software Installation Support - Help with setup and troubleshooting

🏅 Certificate of Completion - Official workshop certificate

💻 Hands-on Practice Files - Real datasets for practice

👨‍🏫 Expert Instructor Support - Direct access to instructors

⭐ Workshop Highlights

🎯 Beginner-friendly approach with step-by-step guidance

💻 Hands-on practical sessions every single day

📊 Real molecular examples from drug discovery

🔬 Industry-standard software tools and pipelines

👨‍🏫 Expert instructors with extensive research experience

📈 Career advancement skills in computational chemistry

Ready to Get Started

Join this comprehensive workshop and master computational drug design!

Registeration Closed Contact Us

10-Day Online Workshop: Computational Drug Design, Molecular Docking & MD Simulation

📅 Duration

⏰ Time

💻 Format

📚 Sessions