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.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# 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 artifacts in the run output folder (`outputs/`).
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.
The line at the top of this page pins the label git:20260930.9b33ccf, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
GET https://markdownregistry.com/api/v1/artifacts/art_jqjmkvs2knxlka3v
GET https://markdownregistry.com/api/v1/resolve?ref=yichen-zju/claude-for-research/diffdock
GET https://markdownregistry.com/api/v1/blob/b311a5d33e968822972c1bc44f8d01b43363f919cd5d7e27337086a6b89516a4
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