Dates: October 12-18, 2024

Time: 7:00 PM – 8:00 PM IST

Discounted Price: ₹1800/- for Indian participants | $30 for international participants.

This workshop is tailored for beginners who are interested in learning molecular docking from scratch. You will learn how to prepare proteins and ligands, set up docking experiments, optimize the docking procedure and analyze results in a simple, easy-to-follow manner.

Payment Link for Indian Participants: https://rzp.io/rzp/DockingSeries

Payment Link for International Participants: PayPal Link

Agenda

Day 1: Introduction to Molecular Docking

• Overview of Molecular Docking
  • Definition and significance in drug discovery
  • Key concepts: receptor, ligand, binding affinity, binding site
• Fundamentals of Protein-Ligand Interactions
  • Types of interactions: hydrogen bonds, hydrophobic interactions, electrostatic interactions
• Software and Tools for Docking
  • Overview of popular docking software (AutoDock, Vina)
  • Introduction to auxiliary tools (AutoDockTools, Maestro)

Days 2-4: Simple Docking Using AutoDock

• Introduction to AutoDock
  • Overview of AutoDock and its capabilities
  • Installation and setup
• Preparing the Receptor
  • Obtaining and cleaning the PDB structure
  • Adding hydrogen atoms and assigning charges
• Preparing the Ligand
  • Obtaining and drawing the ligand structure
  • Adding hydrogen atoms, assigning charges, and defining rotatable bonds
• Setting Up the Docking Experiment
  • Defining the grid box parameters
  • Configuring docking parameters and running AutoDock
• Analyzing Docking Results
  • Interpreting binding poses and scoring results
  • Visualizing interactions using Maestro, Discovery Studio, etc.
• Multi-Ligand Docking
  • Ligand database preparation
  • Multiple ligands docking using AutoDock Vina, PyRx, and automation with Python scripts

Day 5: Choosing the Right PDB or Target Structure

• Selecting the Appropriate PDB Structure
  • Criteria for selecting high-quality crystal structures
  • Evaluating structure resolution and completeness
• Addressing Missing Residues or Undetermined Structures
  • Homology modeling techniques (SWISS-MODEL, Modeller)
  • Refinement and validation of modeled structures

Day 6: Docking Without a Known Binding Site

• Binding Site Prediction Tools
  • Overview of site prediction tools (MetaPocket, CASTp, FTMap)
  • Practical demonstration of using these tools to identify potential binding sites
• Database Search
  • Utilizing databases and resources for binding site information

Day 7: Validating the Docking Protocol

• Redocking for Validation
  • Importance of redocking in validating docking protocols
  • Step-by-step guide to performing redocking and comparing results
• Q&A and Troubleshooting
  • Addressing common issues and challenges in docking
  • Open discussion and expert advice on specific problems