Agent Skill
Diffdock skill
diffdockaipoch/open-scienceresources/skills/diffdock/SKILL.md
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.
always on
111 tokname + description
once used
938 tokSKILL.md body
bundled files
22 KB
repo stars
5.3kGitHub
Install the Diffdock skill
Skills CLI (Claude Code, Codex, Cursor and others)
npx skills add https://github.com/aipoch/open-science --skill diffdock
Claude Code, by hand (all projects)
git clone --depth 1 https://github.com/aipoch/open-science.git /tmp/open-science mkdir -p ~/.claude/skills cp -R /tmp/open-science/resources/skills/diffdock ~/.claude/skills/diffdock
For one project only, copy the folder into .claude/skills/ in that project instead. The agent picks it up when a task matches its description.
What it costs your context
Agent Skills load in three steps. Tokens counted with the o200k tokenizer; your model's count will differ a little.
| When | What loads | Cost |
|---|---|---|
| Every session | Name and description | 111 tok |
| When the agent uses it | The SKILL.md instructions | 938 tok |
| Only if opened | 2 bundled files (2 KB) | varies |
Until it is used, diffdock costs about 12× less than the median MCP server we measured (1,362 tokens on every turn). Installing all 25 skills from aipoch/open-science would load 2,130 tokens of descriptions. Skills vs MCP study
Checks
Our checks found nothing to flag: it follows the Agent Skills specification's naming and size guidelines and doesn't pipe downloads into a shell.
Checked 2026-10-22 · method
What's inside
The headings of its SKILL.md. Read the full file on GitHub.
- 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 --liganddescription
- Errors worth recognizing
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