diffdock SKILL.md skillA
diffdock from pengqianhan/ai-human-research-os is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pengqianhan/ai-human-research-os/diffdock@git:20260715.38d79bePins git:20260715.38d79be in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pengqianhan/ai-human-research-os
- Path
research-skills-hub/claude-science-skills/skills/diffdock/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260715.38d79be, committed Jul 15, 2026
- Size
- 4,476 bytes
- Repository stars
- 3
- License
- MIT
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.
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-L DiffDock-L is a blind pose predictor: given a protein structure and a ligand, it samples ligand placements over the whole surface with a diffusion model and ranks them with a separately trained confidence head. The confidence score correlates with pose correctness, not with binding free energy — DiffDock does not predict whether or how tightly the ligand binds, so for hit triage you still pair it with a scorer (GNINA, MM-GBSA) or with `boltz`'s affinity head. For protein–protein and nucleic-acid co-folding, route to `boltz` or `chai1`. Code and weights are MIT (github.com/gcorso/DiffDock). ## Running it ```bash cd $DIFFDOCK_REPO # a clone of github.com/gcorso/DiffDock python3 -m inference \ --config default_inference_args.yaml \ --protein_path target.pdb \ --ligand_description "COc1ccc(C#N)cc1" \ --out_dir out ``` For more than one complex, give `--protein_ligand_csv batch.csv` instead of the two single-complex flags; the CSV has four columns — `complex_name`, `protein_path`, `ligand_description` (SMILES or an `.sdf`/`.mol2` path), and `protein_sequence`. Leave `protein_path` empty and fill `protein_sequence` to …
Read the whole file at its exact version.
How to install
mdr add pengqianhan/ai-human-research-os/diffdock@sha256:6c3acc1710209b8dThe line at the top of this page pins the label git:20260715.38d79be, 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_hdrtbh4kmtshidxp)
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Versions
The registry has recorded 1 version of this file, committed on Jul 15, 2026.
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 (4476 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
pengqianhan/ai-human-research-os · 3 stars · license MIT · pushed 2026-10-19 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_hdrtbh4kmtshidxp GET https://markdownregistry.com/api/v1/resolve?ref=pengqianhan/ai-human-research-os/diffdock GET https://markdownregistry.com/api/v1/blob/6c3acc1710209b8daf2322e6103043c3487412153e2455deab6abd851ad8efb6
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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