fair-esm2 SKILL.md skillA
fair-esm2 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/fair-esm2@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/fair-esm2/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260715.38d79be, committed Jul 15, 2026
- Size
- 4,914 bytes
- Repository stars
- 3
- License
- MIT
Embed proteins with Meta AI's ESM-2 (`fair-esm` package). Use this skill when: (1) Extracting per-residue or per-sequence embeddings for downstream ML, (2) Masked-LM likelihood / mutation effect scoring, (3) Contact prediction from a sequence.
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
# fair-esm2 — ESM-2 (Meta AI)
ESM-2 code and weights are MIT (Meta AI, github.com/facebookresearch/esm).
> **Package disambiguation.** `pip install fair-esm` gives you `import esm`
> with `esm.pretrained.*` (ESM-1/2). Biohub's github.com/Biohub/esm fork
> (MIT) gives you `from esm.models.esmfold2 import ESMFold2InputBuilder` —
> see the **`esmfold2`** skill. Both share the `esm` namespace but are
> different libraries. This skill covers **fair-esm** (the Meta package).
## Prerequisites
| Requirement | Minimum | Recommended |
| ----------- | ------- | ----------- |
| Python | 3.8+ | 3.11 |
| CUDA | 11.7+ | 12.x |
| GPU VRAM | 8 GB (8M), 16 GB (650M) | 24 GB+ (650M / 3B) |
## How to run
### Embeddings
```python
import torch, esm
model, alphabet = esm.pretrained.esm2_t33_650M_UR50D()
model = model.eval().cuda()
bc = alphabet.get_batch_converter()
_, _, toks = bc([("ubq", "MQIFVKTLTGKTITLEVEPSDTIENVK")])
with torch.no_grad():
out = model(toks.cuda(), repr_layers=[33])
emb = out["representations"][33] # (1, L+2, 1280) — includes BOS/EOS
seq_emb = emb[0, 1:-1].mean(0) # per-sequence mean
```
### Masked-LM scoring
```python
…Read the whole file at its exact version.
How to install
mdr add pengqianhan/ai-human-research-os/fair-esm2@sha256:ab851af1124c563bThe 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_l7uzohvfy3lwnhwi)
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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
- 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
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- 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_l7uzohvfy3lwnhwi GET https://markdownregistry.com/api/v1/resolve?ref=pengqianhan/ai-human-research-os/fair-esm2 GET https://markdownregistry.com/api/v1/blob/ab851af1124c563b183e4d98fc6891cc289a61b83a5dd4145618970b6942ece5
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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