Learn Molecular Docking From The Scratch

Learn how to install the molecular docking software across Windows, Linux, and macOS, including selecting the right Python version, installing Python packages, and following setup steps.

Learn to locate protein structures in public databases and download pdb files for docking. Refine retrieved molecules by removing unwanted residues and preparing accurate coordinates for docking experiments.

Practice preparing a protein for docking by loading the structure, adding hydrogens, adjusting charges, and converting the data into a docking-ready input format for accurate grid-based docking.

Learn how to prepare the ligand for docking by configuring options and parameters, saving the prepared ligand, and managing box space and PDB settings.

Learn how to fix the grid around the active site and perform AutoGrid. Set grid dimensions and map types, then save the file for docking.

Learn to perform docking with AutoDock by selecting the ligand, configuring docking parameters, and running a quick search to obtain and interpret the docking energy output.

Evaluate docking results by comparing binding energy and analyzing protein–ligand conformations, hydrogen bonds, and hydrophobic interactions, then export the best pose to pdb and pdbqt formats.