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One-Week Workshop on
Computer-Aided Drug Design, Molecular Docking & MD Simulation

A comprehensive 7-day hands-on program covering the complete CADD pipeline — from target identification and virtual screening to molecular docking and MD simulation analysis.

📅 Duration

May 1 – 7, 2026

⏰ Time

7:30 PM – 9:00 PM (IST)

💻 Format

Online Hands-On

🎓 Level

Beginner – Intermediate

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About the Workshop

This one-week intensive workshop takes participants through the complete Computer-Aided Drug Design (CADD) pipeline using industry-standard tools. Starting from drug discovery fundamentals and database navigation, the program progresses through virtual screening, protein and ligand preparation, molecular docking, results analysis, and finally molecular dynamics simulation and trajectory analysis.

Every day combines theory with hands-on practical sessions, ensuring participants gain both conceptual understanding and real-world software skills applicable to academic research and pharmaceutical industry workflows.

👥 Who Should Attend?

Ideal for undergraduate and postgraduate students, PhD scholars, faculty members, and researchers in bioinformatics, pharmacy, biotechnology, chemistry, and life sciences who want practical CADD skills for research or career advancement.

📚 Complete 7-Day Curriculum

Day 1 Introduction to Drug Discovery & CADD

📖 Theory

  • Drug discovery pipeline
  • Target identification vs target validation
  • Role of bioinformatics in drug discovery
  • Databases used in drug discovery
  • Structure-based vs ligand-based drug design
  • Case studies of CADD

🔬 Practical

  • UniProt — Protein sequence retrieval
  • PDB — Structure retrieval
  • PubChem — Ligand retrieval
  • DrugBank — Drug information
Day 2 Virtual Screening & ADMET

📖 Theory

  • Virtual screening workflow
  • Ligand-based vs structure-based screening
  • Lipinski Rule of 5
  • Drug-likeness
  • ADMET properties
  • Toxicity prediction

🔬 Practical

  • SwissADME
  • ADMETSar
  • Virtual screening using PyRx
Day 3 Protein & Ligand Preparation

📖 Theory

  • Protein structure basics
  • Homology modeling basics
  • Protein cleaning and preparation
  • Ligand drawing and optimization
  • Energy minimization
  • File format conversion (PDB, MOL2, PDBQT)

🔬 Practical Tools

  • Chimera / ChimeraX
  • Open Babel
  • ChemSketch
  • PyRx
Day 4 Molecular Docking — Theory & Setup

📖 Theory

  • Molecular docking principles
  • Rigid vs flexible docking
  • Scoring functions
  • Binding affinity
  • Grid box setup
  • Docking parameters

🔬 Practical

  • AutoDock Tools
  • AutoDock Vina
  • Preparing receptor & ligand
  • Grid box setup
  • Running docking
Day 5 Docking Results Analysis

📖 Theory

  • Binding energy interpretation
  • Hydrogen bonds
  • Hydrophobic interactions
  • RMSD
  • Interaction analysis

🔬 Practical

  • PyMOL visualization
  • Discovery Studio Visualizer
  • ChimeraX
  • Interaction analysis
  • Docking result interpretation
Day 6 Molecular Dynamics Simulation

📖 Theory

  • Molecular dynamics basics
  • Force fields (AMBER, CHARMM, OPLS)
  • System preparation
  • Solvation and ion addition
  • Energy minimization
  • NVT and NPT equilibration
  • Production run

🔬 Practical

  • GROMACS installation
  • System setup
  • Running MD simulation
Day 7 MD Analysis & Case Study

📖 Theory

  • RMSD
  • RMSF
  • Radius of gyration
  • Hydrogen bond analysis
  • Free energy calculations
  • Real-world case studies

🔬 Practical

  • Trajectory analysis
  • Visualization using VMD / PyMOL
  • Result interpretation
  • Case study project

Workshop Registration Fee

UG / PG Student

₹1099 INR

PhD Scholar / Researcher

₹1499 INR

Faculty

₹1999 INR

Includes: Recordings • Study Materials • Certificate • Software Support

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📥 Study Materials & Resources

All workshop resources will be made available to registered participants. Download links will be activated after registration.

📦

Workshop Study Materials

Slides, protocols & datasets

Available
📄

Pre-Workshop Requirements

Software setup & prerequisites

🔒 Coming Soon
📋

Workshop Handout

Daily reference guide

🔒 Coming Soon

💡 Once the ZIP file is ready, the download button will be activated. Registered participants will also receive materials directly via email.

🛠️ Tools & Software Used

All software used in this workshop is freely available. Installation guides will be shared before the workshop begins.

🧬 AutoDock Vina
🔬 GROMACS
🖥️ PyMOL
🧪 UCSF ChimeraX
💊 Discovery Studio
🔁 Open Babel
✏️ ChemSketch
🌐 SwissADME
📊 PyRx
🎬 VMD

👥 Who Should Attend

✓ UG/PG students in pharmacy, bioinformatics, or chemistry
✓ PhD scholars needing CADD skills for research
✓ Faculty in computational chemistry or drug design
✓ Researchers entering computational drug discovery
✓ Industry professionals in pharma/biotech R&D

🎯 Learning Outcomes

✓ Navigate drug discovery databases confidently
✓ Perform ADMET screening and virtual screening
✓ Prepare proteins and ligands for docking
✓ Execute and interpret molecular docking results
✓ Run and analyse MD simulations using GROMACS

✨ What's Included

🎥 Recorded Sessions — All 7 days on-demand
📦 Study Material ZIP — Slides, protocols & datasets
🛠️ Software Setup Support — Pre-workshop installation help
🏅 Certificate of Completion — Official workshop certificate
🧬 Real Biological Datasets — Hands-on with authentic data
👨‍🏫 Expert Instructor Support — Live Q&A every session