Video Tutorial Docking Molekuler Dengan Aplikasi Autodock

In this video, the presenter introduces molecular docking simulations, starting with the basic concepts of molecular docking and its purpose, which includes predicting ligand binding and discovering new ligands through virtual screening. They highlight the importance of software tools needed for this simulation process, such as MDL tools, Discovery Studio, and AutoDock, and explain their roles in preparing ligands and proteins for the docking process.

The first step outlined by the presenter is to create a dedicated folder for the docking process and locate the target macromolecule protein from online databases, such as the RCSB PDB. They demonstrate how to find a specific protein’s PDB ID and the structural details necessary for preparing the protein-ligand complex.

After preparing the docking folder, the presenter emphasizes the need to visualize and clean up the downloaded structure using Discovery Studio, which includes removing water molecules and unnecessary residues. They illustrate how to modify the visual representation to focus on the protein and the ligand to be docked, such as ibuprofen, ensuring the structure is ready for the next steps.

In the next segment, the focus shifts to using AutoDock software to prepare molecules for docking. The presenter details the process of adding hydrogen atoms, setting the charge states, and saving the protein and ligand in the correct formats. They explain how this preparation is crucial for the accuracy of the docking simulation results.

Moving forward, the presenter discusses setting up the docking parameters, including defining the grid box around the protein where the ligand will bind. They walk through the process of inputting necessary files, configuring the algorithm, and starting the docking run, which can take time based on the number of docking attempts set in the simulation.