proteinmpnn SKILL.md skillA
proteinmpnn from aipoch/open-science is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add aipoch/open-science/proteinmpnn@git:20260814.c9a70d8Pins git:20260814.c9a70d8 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- aipoch/open-science
- Path
resources/skills/proteinmpnn/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260814.c9a70d8, committed Aug 14, 2026
- First version recorded
- Jul 14, 2026
- Size
- 5,258 bytes
- Repository stars
- 5,279
- License
- Apache-2.0
Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, github.com/dauparas/ProteinMPNN). Reach for this skill to run sequence design on RFdiffusion backbones, to redesign one chain of a PDB while holding interface residues fixed, or to generate a temperature-swept set of sequences for downstream folding.
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
# ProteinMPNN ProteinMPNN is the default inverse-folding step in the binder pipeline: a message-passing network that sees backbone geometry only, so it is the right choice when the design surface is protein–protein and the wrong one as soon as a ligand, nucleic acid, or metal is part of the interface — `ligandmpnn` adds those atoms to the graph with a near-identical CLI, and `solublempnn` swaps in weights trained on soluble structures for an expression-biased prior. Code and weights are MIT (github.com/dauparas/ProteinMPNN). The model is small enough to run on CPU — for a handful of sequences on one backbone that is seconds and usually faster than dispatching a remote job; a GPU helps for batched campaigns (hundreds of backbones or large `--num_seq_per_target`). Either way the repo is cloned in-job — there is no PyPI dist and the checkpoints are bundled in the repo. ## Running it ```bash pip install torch numpy # if not already present git clone --depth 1 https://github.com/dauparas/ProteinMPNN.git proteinmpnn cd proteinmpnn python protein_mpnn_run.py \ --pdb_path backbone.pdb --pdb_path_chains "A" \ --out_folder out --num_seq_per_target 16 --sampling_temp "0.1" ``` …
Read the whole file at its exact version.
How to install
mdr add aipoch/open-science/proteinmpnn@sha256:fb284aced53d394bThe line at the top of this page pins the label git:20260814.c9a70d8, 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_qaqzdxo3flu5duup)
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Versions
The registry has recorded 2 versions of this file, between Jul 14, 2026 and Aug 14, 2026, about one every 31 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260814.c9a70d8 latest | 2026-08-14 | c9a70d8 | 5,258 B | A | view · diff |
| git:20260714.a2a3282 | 2026-07-14 | a2a3282 | 4,587 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 (5258 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
aipoch/open-science · 5,279 stars · license Apache-2.0 · pushed 2026-10-19 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_qaqzdxo3flu5duup GET https://markdownregistry.com/api/v1/resolve?ref=aipoch/open-science/proteinmpnn GET https://markdownregistry.com/api/v1/blob/fb284aced53d394b82411b022ab00ff1da07be2fd16da4d4d08d28d6e74540ba
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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