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 series of grids that describe the target protein; and the other Auto Grid precalculates these grids. In addition to using them for docking, you can visualize atomic affinity grids. A graphical user interface called Auto Dock Tools or ADT was used to generate grids, calculate the dock score, and evaluate the conformers. Rasmol:RASMOL [Raster Display of Molecules] is a molecular graphics program intended for the 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 combinations. DOCKING METHODOLOGY: The structure of β-ketoacyl-acyl synthase (KAS) transporter protein, which is an essential target for designing new antibacterial drugs was retrieved from the PDB [10]. A 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 tasks. The molecules selected for docking studies are from the selected article [11, 12]. Docking studies were conducted on the ecKAS III receptor (pdb id: 1HNJ). All these molecules, as well as the bound ligand of the 1HNJ protein, were docked using Auto Dock software and the score values ​​were predicted. Interactions of protein ligands were also studied. All molecules were drawn using the ChemDraw Ultra 8.0 tool and energy was minimized using the Chem 3D Ultra 8.0 software. Automated docking was used to locate the ap… at the center of the paper… with this method the ligands were manually held in the receptors and minimized to reduce steric clashes between the atoms in the molecule. Nowadays, docking is done using recent computational resources. Recent docking studies involve systemic 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 nucleus. Random Method: This method involves simultaneous changes of a ligand molecule. The evaluated ligands will be used for subsequent steps. Simulation method: In this method both the target and the ligand are treated as flexible. In this method the ligand preparation is mapped onto a grid. Then the grid energy values ​​are minimized to fix the ligand into a receptor.