proteinmpnn SKILL.md skillA
proteinmpnn 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/proteinmpnn@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/proteinmpnn/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260715.38d79be, committed Jul 15, 2026
- Size
- 4,587 bytes
- Repository stars
- 3
- License
- MIT
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 pengqianhan/ai-human-research-os/proteinmpnn@sha256:9873f4f800d457a6The 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_egu3km7che6s3h7h)
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Versions
The registry has recorded 1 version of this file, committed on Jul 15, 2026.
Audit of the latest version
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- 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
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- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
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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_egu3km7che6s3h7h GET https://markdownregistry.com/api/v1/resolve?ref=pengqianhan/ai-human-research-os/proteinmpnn GET https://markdownregistry.com/api/v1/blob/9873f4f800d457a6b6a7139df133e8b4b259694c9433e188ca551929373f47b8
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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