Multi Ligand Docking Using AutoDock Vina COX 2 Virtual Screening Tutorial

Multi-Ligand Docking Using AutoDock Vina | COX-2 Virtual Screening Tutorial In this tutorial, we will perform multi-ligand molecular docking of 10 established COX-2 inhibitors using AutoDock Vina. The workflow demonstrates how multiple ligands can be prepared, docked automatically using a Perl script, and subsequently analyzed through docking scores, binding poses, and protein–ligand interactions. The target used in this tutorial is Cyclooxygenase-2 (COX-2) using PDB ID: 3LN1, a crystal structure of celecoxib bound at the COX-2 active site. 🧬 Complete workflow covered 1. Ligand preparation Open Babel AutoDock Tools Preparation of 10 COX-2 inhibitors 2. Protein preparation COX-2 structure: PDB 3LN1 Receptor preparation for molecular docking 3. Grid preparation Identification of the COX-2 active site Definition of docking/grid coordinates 4. Automated multi-ligand docking AutoDock Vina Perl scripting Sequential docking of 10 ligands Automated output organization and score extraction 5. Docking result comparison Comparison of predicted docking scores Ranking of the docked compounds 6. Pose visualization PyMOL / BIOVIA Discovery Studio Visualization of ligand binding poses inside the COX-2 active site 7. Protein–ligand interaction analysis Identification of surrounding amino-acid residues Hydrogen-bond and hydrophobic interaction analysis 2D interaction visualization 💊 Ligands used The tutorial includes: Celecoxib Rofecoxib Valdecoxib Etoricoxib Lumiracoxib Meloxicam Nimesulide Diclofenac Indomethacin SC-558 💻 Software used Open Babel (https://sourceforge.net/projects/openbabel/) BIOVIA Discovery Studio AutoDock Tools AutoDock Vina Perl (https://padre.perlide.org/) PyMOL #MolecularDocking #AutoDockVina #COX2 #VirtualScreening #DrugDiscovery #ComputationalChemistry #Bioinformatics #MolecularModeling #Perl #PyMOL #AutoDockTools #OpenBabel #DiscoveryStudio #COX2Inhibitors #InSilicoDrugDiscovery