diffdock

by aipoch5.0k

Install

The skill file stays in the publisher's repository.

Paste the copied command in a terminal. It installs this SKILL.md into that agent.

npx skills add aipoch/open-science --skill diffdock -a cursor -y

Download skill resources/skills/diffdock/SKILL.md on GitHub

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How do I install diffdock?: Download resources/skills/diffdock/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does diffdock live?: The publisher keeps it at https://github.com/aipoch/open-science.
Which agents can use diffdock?: Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.

name: diffdock description: > Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind diffusion docking that places a ligand into a protein pocket without a predefined search box and ranks the samples with a learned confidence model. Reach for this skill to dock a SMILES or SDF against a PDB, to generate ranked 3D poses for a small fragment library, or to get a starting pose for downstream rescoring. DiffDock predicts geometry, not affinity. license: Apache-2.0 category: biomodels requirements: [gpu] metadata: display-name: DiffDock

You see	It means / do this
`ValueError: not allowed to raise maximum limit` at startup	`setrlimit(NOFILE, 64000)` exceeds the sandbox hard limit — `sed` the constant in `inference.py` to `min(64000, rlimit[1])`.
Silent SIGKILL a few minutes into the SO(3) precompute	Host RAM exhausted — see the gotcha above.
`python3: not found`	You are on the upstream `rbgcsail/diffdock` image — that one runs from `/home/appuser/DiffDock` under `micromamba`.

diffdock

Install

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github.com/gcorso/DiffDock/blob/main/LICENSE: MIT (© 2022 Corso, Stärk,

Jing). verified 2026-06-30

third_party: - kind: weights name: DiffDock-L license: MIT terms_url: https://github.com/gcorso/DiffDock/blob/main/LICENSE

DiffDock-L

Running it

The YAML config overwrites your CLI flags

The first run is silent for ~11 minutes and needs ≥32 GB host RAM

The README's `--ligand` works on the CLI by accident — use `--ligand_description`

Errors worth recognizing

Install

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github.com/gcorso/DiffDock/blob/main/LICENSE: MIT (© 2022 Corso, Stärk,

Jing). verified 2026-06-30

third_party: - kind: weights name: DiffDock-L license: MIT terms_url: https://github.com/gcorso/DiffDock/blob/main/LICENSE

DiffDock-L

Running it

The YAML config overwrites your CLI flags

The first run is silent for ~11 minutes and needs ≥32 GB host RAM

The README's --ligand works on the CLI by accident — use --ligand_description

Errors worth recognizing

The README's `--ligand` works on the CLI by accident — use `--ligand_description`