Autodock Vina
K-Dense-AI/drug-discovery-agent-skillsStructure-based docking with AutoDock Vina, Vinardo, and AutoDock4 through the Meeko toolchain. Use this skill to define a docking box, prepare receptors and ligands as PDBQT, run single or batch docking, rescore, and interpret affinities, poses, and ligand efficiency. Covers box definition from a reference ligand or pocket residues, protonation and tautomer decisions, flexible side chains, exhaustiveness and seeds, redocking validation, and virtual screening over compound libraries. Also trigger on vina, smina, gnina, mk_prepare_ligand, mk_prepare_receptor, mk_export, scrub.py, PDBQT, autogri...
At a glance
This skill is for Research and helps you prepare receptors and ligands for molecular docking, run protein-ligand docking with autodock vina, and perform virtual screening on compound libraries.
git clone --depth 1 https://github.com/K-Dense-AI/drug-discovery-agent-skills
cp -r drug-discovery-agent-skills/skills/autodock-vina ~/.claude/skills/autodock-vina
Autodock VinaMolecular Dockingdrug-discoveryPdbqtStructure BasedVirtual Screening
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