docking-vina

Goal

To perform molecular docking of one or more small-molecule ligands into a protein receptor using AutoDock Vina (>= 1.2.x) via its Python API, producing:

• Ranked binding poses (PDBQT)
• Docking scores (kcal/mol) and pose RMSDs
• A machine-readable JSON report with full docking parameters for reproducibility

This skill is intended for pose generation and relative ranking, not rigorous binding free energy prediction. Please refer to the original Vina method (Trott & Olson, https://doi.org/10.1002/jcc.21334) and the AutoDock Vina repo (https://github.com/ccsb-scripps/AutoDock-Vina) for more details.

Instructions

1. Prepare receptor and ligand (recommended)

Docking accuracy is strongly affected by structure preparation (protonation, missing residues, cofactors, waters, tautomer states, etc.). Use:

• protein-prep to generate *_prepared.pdbqt
• ligand-prep to generate ligand *.pdbqt (consider multiple protomers/tautomers)