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

  • Thermodynamics and kinetics of binding

• Software and Tools for Docking

  • Overview of popular docking software (AutoDock, Vina)

  • Introduction to auxiliary tools (AutoDockTools, Maestro, Discovery Studio)

Day 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 using python Script.

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

• Protein Preparation Best Practices

  • Removing water molecules and other non-relevant entities

  • Ensuring proper protonation states and charge assignments

Day 6: Docking Without a Known Binding Site

• Blind Docking Approach

  • Principles and challenges of blind docking

  • Practical steps for performing blind docking using AutoDock

• 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