AutoDock Vina Molecular Docking

Overview

AutoDock Vina is one of the fastest and most widely used open-source molecular docking engines for predicting protein–ligand binding modes and affinities. This skill covers the full Python-based pipeline: receptor preparation from PDB, ligand preparation from SMILES/SDF via Meeko and RDKit, search box definition, docking execution, pose analysis, and batch virtual screening for hit identification.

When to Use

• Predicting binding poses of small molecules to a protein target
• Estimating relative binding affinities (kcal/mol) for ligand ranking
• Virtual screening of compound libraries against a target receptor
• Validating docking protocols by re-docking co-crystallized ligands
• Preparing docking inputs from SMILES strings without intermediate files
• Comparing binding modes of analogs in a structure-activity relationship study
• Generating starting poses for molecular dynamics simulations
• Use DiffDock instead for blind docking when the binding site is unknown; use GNINA as an alternative with CNN scoring

Prerequisites