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Course Content
Class 01: Introduction to CADD and Molecular Docking:
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What is Computer-Aided Drug Design?
The role of Protein-Ligand Interactions in biology.
Types of docking (rigid, semi-flexible, and flexible).
Class 02: Preparing Molecular Structures:
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Finding and downloading Protein Data Bank (PDB) structures.
Ligand preparation (2D to 3D conversion, energy minimization).
Protein preparation (adding hydrogens, removing water, defining the active site).
Class 03: Executing the Docking Simulation:
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Introduction to open-source software (e.g., AutoDock Vina).
Setting up the docking grid box parameters.
Running the simulation and generating binding poses.
Class 04: Analyzing and Interpreting Results:
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Understanding the binding affinity/docking score (e.g., $\text{kcal/mol}$).
Visualizing protein-ligand interactions (hydrogen bonds, hydrophobic contacts) using PyMOL or similar software.
Identifying the most favorable binding pose.
Class 05: Applications and Next Steps:
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Case studies of successful drug discovery using docking.
Introduction to Virtual Screening and high-throughput docking.
Further reading and resources.
Free Course on Protein-Ligand Molecular Docking
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