Diffdock

Run or plan DiffDock molecular docking workflows. Use when a task asks for protein-ligand pose prediction, docking setup, ligand/protein preparation, pose ranking, or docking-result verification.

advaitpaliwal f394c2b 963 B Updated

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DiffDock

Use this skill for protein-ligand docking and pose review.

Workflow:

  1. Record protein source, chain selection, binding site context, ligand identity, protonation/tautomer assumptions, and known cofactors.
  2. Verify the available execution path and dependency stack before claiming a docking run is possible.
  3. Preserve input PDB/mmCIF, ligand SDF/SMILES, prepared structures, command, seed, package version, and logs.
  4. Save ranked poses, confidence scores, contact summaries, and 3D previews as Feynman artifacts.
  5. Compare poses against known ligands, active-site residues, experimental structures, or orthogonal docking where the conclusion matters.

Report docking as a ranked hypothesis, not binding proof.

advaitpaliwal/feynman/tree/main/skills/diffdock commit f394c2bba9

Frequently asked questions

npx skillmds@latest add advaitpaliwal/diffdock