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diffdock

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Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose triage, confidence interpretation, and validation. Use for molecular docking and virtual-screening pose generation, not binding-affinity prediction.

skills/diffdock/SKILL.md

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Last checked
Nov 10, 2026

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Nov 9, 2026
License
MIT

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# DiffDock: protein-small-molecule docking

DiffDock-L generates candidate ligand poses and ranks them by model confidence.
Confidence is neither a measured probability of correctness nor binding affinity.
Use this skill for one pair, batches, or separate receptor conformations; treat
library-wide confidence sorting as pose triage, not hit identification.

## Verified scope

Targets the current [v1.1.3 release](https://github.com/gcorso/DiffDock/releases/tag/v1.1.3).
Released source and current main's identical `inference.py` were checked on
2026-09-30. Bundled helpers were tested on tiny synthetic inputs; pretrained docking,
ESMFold, CUDA, Docker, GNINA, and hosted-demo execution were **not** run in this
review. Commands requiring those components are source-verified recipes, not
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