diffdock SKILL.md skillA
diffdock from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/diffdock@v1.6Pins v1.6 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/diffdock/SKILL.md- Versions recorded
- 8
- Latest version
- v1.6, committed Oct 1, 2026
- First version recorded
- Jun 7, 2026
- Size
- 11,830 bytes
- Repository stars
- 53,159
- License
- MIT
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.
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: 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 successful end-to-end demonstrations. ## Set up the upstream environment ```bash git clone --branch v1.1.3 --depth 1 https://github.com/gcorso/DiffDock.git cd DiffDock conda env create --file environment.yml conda activate diffdock ``` The upstream environment pins Python 3.9.18, CUDA 11.7 Torch/PyG wheels and old scientific dependencies. Do not substitute current `torch` or the unrelated PyPI …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/diffdock@sha256:5fafc5d9f53fa35aThe line at the top of this page pins the label v1.6, 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.
[](https://markdownregistry.com/a/art_5omrm32lml5wtqte)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 8 versions of this file, between Jun 7, 2026 and Oct 1, 2026, about one every 17 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.6 latest | 2026-10-01 | a92663a | 11,830 B | A | view · diff |
| v1.5 | 2026-09-30 | a0aea74 | 17,632 B | A | view · diff |
| v1.4 | 2026-09-30 | ce9e6e9 | 17,632 B | A | view · diff |
| v1.3 | 2026-09-02 | 1e5eeff | 17,354 B | A | view · diff |
| v1.2 | 2026-07-28 | 4fb7e0b | 16,408 B | A | view · diff |
| v1.1 | 2026-07-26 | b085e11 | 16,408 B | A | view · diff |
| git:20260611.1b8fae3 | 2026-06-11 | 1b8fae3 | 16,437 B | A | view · diff |
| v1.1 | 2026-06-07 | 758bad1 | 16,432 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (11830 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
k-dense-ai/scientific-agent-skills · 53,159 stars · license MIT · pushed 2026-10-19 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_5omrm32lml5wtqte GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/diffdock GET https://markdownregistry.com/api/v1/blob/5fafc5d9f53fa35a47c498f1cf3bad20fbee7404f248226e76e62bb327749912
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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