autodock-vina-docking

name	autodock-vina-docking
description	Run reproducible local protein-ligand docking with AutoDock Vina and Meeko. Use for pose generation, redocking, or small virtual screens when a receptor and a justified binding pocket are available; do not use a Vina score as experimental affinity.
license	MIT

AutoDock Vina Docking

Gate and preflight

Follow $cx-compute-environment and ask once before installing pinned Vina, Meeko, or preparation dependencies and before compute. Require $cx-molecular-input-preparation outputs and an explicit pocket definition.

Workflow

1. Record Vina/Meeko versions, receptor state, ligand microstates, box center and size in Å, exhaustiveness, modes, energy range, CPU count, and seed.
2. Smoke-test one ligand. Confirm the search box encloses the intended pocket and each ligand can rotate without clipping.
3. Run a positive-control redock before screening. Keep raw PDBQT, log, config, and converted SDF poses under artifacts/<run-id>/vina/.
4. For a screen, process each ligand state independently and preserve failures; never silently keep only successful molecules.
5. Rank poses and compounds separately. Report pose diversity and interactions, then apply $cx-docking-validation.

Interpretation

• Vina energy is a model score, not a measured binding free energy or IC50/Kd.
• Pose success requires a prespecified criterion, commonly top-k symmetry-aware heavy-atom RMSD to a reference pose when that reference is valid.
• Use cold-target/ligand controls and decoys for comparative screening claims.
• Record apo/holo and assembly/template provenance; do not leak a held-out bound pose into pocket construction or ligand initialization.