solublempnn SKILL.md skillA
solublempnn 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/solublempnn@git:20260714.a2a3282Pins git:20260714.a2a3282 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/solublempnn/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260714.a2a3282, committed Jul 14, 2026
- Size
- 4,277 bytes
- Repository stars
- 5,279
- License
- Apache-2.0
Inverse-fold a backbone with SolubleMPNN — ProteinMPNN retrained on a soluble-PDB subset (Dauparas et al. 2022) — for sequences biased toward cytosolic expression and reduced aggregation. Reach for this skill when designs from vanilla ProteinMPNN are aggregating or going to inclusion bodies, when redesigning a membrane-adjacent fold for soluble expression, or when an E. coli expression screen is the next step.
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
# SolubleMPNN SolubleMPNN is not a separate package — it is the ProteinMPNN architecture retrained on a soluble-PDB subset, which shifts the output distribution away from the surface hydrophobics that the full-PDB model happily places (because many of them are buried at crystallographic or membrane interfaces in the training set). Reach for it when the goal is soluble yield in a heterologous host; stick with `proteinmpnn` when native-like recovery matters more, since the soluble prior trades a few points of recovery for the surface bias. Code and weights are MIT (github.com/dauparas/ProteinMPNN, `soluble_model_weights`; also exposed via github.com/dauparas/LigandMPNN). 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 GPU helps for batched campaigns. Either way the repo is cloned in-job (no PyPI dist; checkpoints bundled). ## 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" \ …
Read the whole file at its exact version.
How to install
mdr add aipoch/open-science/solublempnn@sha256:c5c9b5cba2668bfaThe line at the top of this page pins the label git:20260714.a2a3282, 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_cuqf55bkjt7dosqq)
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Versions
The registry has recorded 1 version of this file, committed on Jul 14, 2026.
Audit of the latest version
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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_cuqf55bkjt7dosqq GET https://markdownregistry.com/api/v1/resolve?ref=aipoch/open-science/solublempnn GET https://markdownregistry.com/api/v1/blob/c5c9b5cba2668bfafc54e899e5165a68e07a1425ab25667cab8c86807d3f6e0c
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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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