Cracking the Code: Protein Modelling & Molecular Docking with Bioinformatics Tools

One day workshop - PDM

🔬 Discover the power of structure-based drug design and bring molecules to life—digitally!

🏢 Organized by:

Genomia Diagnostics Research Pvt. Ltd.
 🧬 In Collaboration With
 PDM Technologies

To Register: https://bit.ly/42m5fk3

Fees:499/-

🗓️ Date & Time: 10th May, 2025

Full-Day Intensive | 9:30 AM – 5:30 PM

👥 Who Should Attend?

  • Undergraduate & Postgraduate Students in Life Sciences
  • Research Scholars
  • Aspiring Bioinformaticians & Biotech Professionals
  • Anyone passionate about computational biology or drug discovery!

🎯 Workshop Highlights

Step into the world of bioinformatics-powered drug discovery in this action-packed one-day workshop! This program blends theory, hands-on training, and real-world applications, offering a deep dive into protein structure prediction and molecular docking—two pillars of modern biomedical research.

🧭 Detailed Schedule & Session Overview

🔹 9:30 AM – 10:00 AM: Kickoff & Inspiration
 Start the day with registration and a warm welcome by our organizing team. We’ll outline the objectives of the workshop and give you a glimpse into how bioinformatics is revolutionizing modern drug discovery.

🔹 10:00 AM – 11:00 AM: Protein Modelling – Understanding the Blueprint of Life
 Begin your learning journey with the fundamentals of protein structure—from primary to quaternary levels. Discover how structure drives function, and get introduced to key bioinformatics databases like PDB, UniProt, and NCBI. You’ll also explore essential tools like BLASTp and RCSB-PDB to begin your deep dive into sequence analysis.

🔹 11:00 AM – 11:15 AM: Tea Break – Refresh & Recharge ☕

🔹 11:15 AM – 1:00 PM: Hands-On Homology Modelling – Building Protein Models from Scratch
 Let’s get practical! You’ll retrieve real protein sequences, run BLAST to identify suitable templates, and build your very own 3D protein model using tools like SWISS-MODEL and Phyre2. Once your model is ready, you’ll validate it using powerful analysis tools like Ramachandran Plot and ProSA-web.

🔹 1:00 PM – 2:00 PM: Lunch Break – Bond Over Bioinformatics 🍽️

🔹 2:00 PM – 3:30 PM: Hands-On Molecular Docking – Simulate Drug-Target Interactions
 Now that you’ve built your protein, it’s time to interact with potential drug molecules! Learn how to prepare both ligands and receptors and perform docking simulations using AutoDock Tools, AutoDock Vina, and PyRx. You’ll visualize binding interactions using PyMOL, Discovery Studio, and LigPlot.

🔹 3:30 PM – 3:45 PM: Tea Break – Short Pause, Big Thoughts ☕

🔹 3:45 PM – 5:00 PM: Case Study – Real-World Docking Scenario
 Put everything you’ve learned to the test! Dive into a real case study: docking a known inhibitor with a disease-related target protein. Understand docking scores, analyze hydrogen bonding, and discuss how lead molecules are identified in the drug discovery pipeline.

🔹 5:00 PM – 5:30 PM: The Finale – Quiz, Feedback & Certification 🎓
End the day with a short quiz to reinforce your learning, share your thoughts in the feedback session, and receive your well-deserved certificate of participation.

💻 System Requirements & Setup

Please ensure the following tools are pre-installed on participant systems:

  • 🖥️ PyMOL – 3D Structure Visualization
  • 🔧 AutoDock Tools / PyRx – Docking Environment
  • 🔬 Discovery Studio Visualizer – Interaction Analysis
  • ✅ Internet Connection for Database Access
  • 🧬 Practice Data: Sample Protein Sequences & Ligands (provided by organizer)

🧠 Learning Outcomes

By the end of this workshop, participants will be able to:
✅ Navigate key bioinformatics databases with confidence
✅ Perform protein homology modelling using real sequences
✅ Execute ligand-protein docking simulations
 ✅ Analyze and interpret molecular interactions
✅ Apply computational methods to structure-based drug discovery

💥 Why You Shouldn’t Miss This Workshop

🔹 Gain practical skills demanded in biotech and pharma R&D
🔹 Learn from experienced trainers & domain experts
🔹 Work on real-time case studies that mirror industrial workflows
🔹 Enhance your resume with in-demand computational biology tools

TimeSession TitleDetails & Learning Outcomes
09:30 AM – 10:00 AMRegistration & InaugurationParticipant registration and welcome kits- Opening remarks by organizing committee- Introduction to the workshop objectives and schedule- Brief overview of the role of bioinformatics in modern drug discovery
10:00 AM – 11:00 AMSession 1: Basics of Protein Structure & ModellingUnderstanding protein structure hierarchy (Primary → Quaternary)- Significance of 3D structure in biological function and drug design- Concept of homology modelling- Overview of biological databases: PDB, UniProt, NCBI- Tools introduction: RCSB-PDB for structure retrieval, UniProt for sequence data, and BLASTp for sequence alignment
11:00 AM – 11:15 AMTea BreakRefreshments and informal networking
11:15 AM – 01:00 PMSession 2 (Hands-On): Homology Modelling of ProteinsRetrieving target protein sequence in FASTA format- Identifying suitable templates using BLASTp- Performing homology modelling using SWISS-MODEL and Phyre2- Validating protein models using Ramachandran plots (PROCHECK) and structure analysis (ProSA-web)- Discussion on interpretation of structural accuracy and functional relevance
01:00 PM – 02:00 PMLunch Break
02:00 PM – 03:30 PMSession 3 (Hands-On): Molecular Docking WorkflowIntroduction to molecular docking and its relevance in drug discovery- Preparing protein and ligand structures- Performing docking simulations using AutoDock Tools, AutoDock Vina, and PyRx- Visualizing binding interactions and docking poses using PyMOL, Discovery Studio Visualizer, and LigPlot- Discussing how docking scores correlate with binding affinity
03:30 PM – 03:45 PMTea BreakTea, snacks, and informal discussion
03:45 PM – 05:00 PMSession 4: Case Study & Molecular InterpretationReal-world case study: Docking a known drug candidate with a disease-relevant target protein- Evaluating docking results and interaction profiles- Understanding pharmacophore and binding pocket analysis- Group discussion: How to identify a potential lead compound from docking data
05:00 PM – 05:30 PMWrap-Up & Certificate DistributionRecap quiz on key concepts- Participant feedback and discussion- E-certificate distribution- Group photograph and closing remarks by the hosts
To Register: https://bit.ly/42m5fk3