Auto DockAuto Dock is an automated docking tool. It is designed to predict how small molecules, such as substrates, bind to a receptor of known 3D structures. Auto Dock actually consists of two main programs: one performs ligand docking to a set of grids describing the target protein; and the other Auto Grid precalculates these grids. In addition to using them for docking, atomic affinity grids can be visualized. A graphical user interface called Auto Dock Tools or ADT was used to generate grids, calculate dock score, and evaluate conformers. Rasmol:RASMOL [Raster Display of Molecules] is a molecular graphics program intended for structural visualization of proteins, nucleic acids and small biomolecules. The program reads the molecular coordinate files and interactively displays the molecule on the screen in a variety of representations and color schemes. DOCKING METHODOLOGY: The structure of the carrier protein β-ketoacyl-acyl synthase (KAS), which is an essential target for the design of new antibacterial drugs. was retrieved from PDB [10]. Comparative protein-ligand dock analysis was performed using 1HNJ to evaluate the algorithm and efficiency of the scoring function between Auto Dock 3.0 and experimental activities. The molecules selected for docking studies were taken from the selected article [11, 12]. Docking studies were carried out on the ecKAS III receptor (pdb id: 1HNJ). All these molecules along with the bound ligand of 1HNJ protein were docked using Auto Dock software and the score values ​​are predicted. Protein-ligand interactions were also studied. All molecules were drawn using ChemDraw Ultra 8.0 tool and energy was minimized using Chem 3D Ultra 8.0 software. Automated docking was used to locate the middle of the paper. With this method, ligands were manually maintained in the receptors and minimized to reduce steric conflicts between atoms in the molecule. Nowadays, docking is done by recent computing resources. Recent docking studies involve systems methods, random methods, and simulation methods. Systemic method: In this method, the core fragments are first docked into the binding site of a target molecule. They will be very useful when it is very difficult to interact with the target kernel. Random method: This method involves simultaneous changes of a ligand molecule. The evaluated ligands will be used for the following steps. Simulation method: In this method, the target and ligand are treated to be flexible. In this method, the ligand preparation is mapped onto a grid. Then the energy values ​​of the grid are minimized to fix the ligand in a receptor.