Esm
Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and...
Install
npx skills add K-Dense-AI/scientific-agent-skills --skill esm -g -a claude-code -y- Repository
- K-Dense-AI/scientific-agent-skills55.7k
- Category
- Engineering
- Updated
- 9d ago
- License
- MIT license
- Context cost
- Mediumabout 2,515 tokens
- Runs scripts
- Yes, review before use
What it does
Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding. Applies to local model inference and Biohub hosted clients, including former Forge workflows; distinguishes the separate legacy fair-esm distribution.
ESM: protein generation, embeddings, and folding
When to use
Use for Biohub's esm SDK: ESM3 masked multimodal generation, ESMC sequence
representations, and ESMFold2 all-atom prediction. The former Forge platform
migrated to https://biohub.ai, including ESM3; SDK class names still contain
Forge. This skill targets the released esm 3.4.1.post1, verified against
its wheel and current official documentation.
fair-esm is Meta's separate, older ESM2/ESMFold/ESM-IF distribution. Both
packages import as esm; install them in separate environments. The legacy
esm.pretrained.esm2_* interface is not the Biohub ESMC interface. Hugging Face
Transformers' native ESMC implementation is another API: do not interchange its
version requirements or output types with this SDK.
Setup and model choice
uv venv --python 3.12 .venv-esm
uv pip install --python .venv-esm/bin/python "esm==3.4.1.post1"
The release declares Python >=3.12, Torch >=2.11,<2.12 and Transformers
=4.57.6,<5. Python 3.12, Torch 2.11.0 and Transformers 4.57.6 were tested on CPU. Linux x86_64 installs include GPU-specific dependencies; use a supported inference machine and budget disk space. Flash Attention is optional; it is unnecessary for the tiny CPU tests. Do not install this stack into a shared environment containing incompatible Transformers or Torch pins.
| Task | Local model/API | Hosted client/model |
|---|---|---|
| ESM3 sequence/structure/function generation | ESM3.from_pretrained("esm3-sm-open-v1") | client("esm3-medium-2024-08"); small/large IDs in the ESM3 reference |
| ESMC embeddings | EsmcForMaskedLM and EsmcTokenizer; biohub/ESMC-300M, biohub/ESMC-600M, biohub/ESMC-6B | esmc_client("esmc-600m-2024-12"); 300M/6B also documented |
| ESMFold2 all-atom structures | EsmFold2Model, ESMFold2InputBuilder; biohub/ESMFold2 | esmfold2_client("esmfold2-fast-2026-05") |
