Advancements in bioinformatics have greatly enhanced our ability to predict molecular interactions between proteins and ligands, crucial for drug discovery and development. This study focuses on the implementation and refinement of a computational protocol using AutoDock 4.2 for predicting protein-ligand interactions. The protocol begins with acquiring and preparing PDB and PDBQT format files, followed by grid and docking parameter file preparation using AutoDock tools. Molecular docking simulations were conducted using Cygwin, and the results were comprehensively analyzed