# 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.

- Skill: `advaitpaliwal/diffdock` (Agent Skill)
- Install (CLI): `npx skillmds@latest add advaitpaliwal/diffdock`
- Raw SKILL.md: https://api.skillmd.com/api/skills/advaitpaliwal/diffdock/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Productivity
- Author: advaitpaliwal (https://skillmd.com/u/advaitpaliwal)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/advaitpaliwal/diffdock

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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.