Forsy Agent
Use case
Guides setup, execution, and validation of an AutoDock Vina docking run for a protein target with a co-crystallized ligand: verifying the toolchain (vina, Python, rdkit/meeko/scipy/gemmi, optional Open Babel/MGLTools), downloading receptor PDB and ligand 3D SDF, parsing structural state (atom counts, waters, per-chain counts, ligand centroid/span, binding-site residues), choosing receptor chains from measured distances and biological-assembly evidence, defining an evidence-based anisotropic search box, preparing PDBQT via Meeko, writing a rerunnable config with fixed seed, running Vina, and validating poses by centroid offset and 4 A contact recovery rather than score alo…
Outcome
The evaluated tasks performed better with this skill. Results apply to the tasks tested.