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ESM Protein Language Model Skill

Helps you write correct ESM3, ESMC, and Forge/Biohub code for protein generation, folding, and embeddings.

Dev & CodingAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

Guides Claude to use the right classes, model IDs, and parameters in EvolutionaryScale's esm Python SDK.

  • ESM3 generation: fill masked positions (_), create variants, function-conditioned design
  • Structure prediction & inverse folding: get 3D coordinates, export PDB, design sequences from a backbone
  • ESMC embeddings: local esmc_300m / esmc_600m inference with batching patterns
  • Hosted Forge/Biohub inference: esm.sdk.client() with ESM_API_KEY, async batch via async_generate
  • Model selection guide: 1.4B open weights up to 98B hosted, with quality/speed/cost tradeoffs
  • Reference files: esm3-api, esm-c-api, forge-api, biohub-platform (ESMFold2), and end-to-end workflows loaded on demand

It also enforces good hygiene: never hardcode API keys, pin endpoints to trusted hosts, and follow the Responsible Biodesign framework.

Who it's for

  • Protein engineering and drug discovery researchers
  • ML engineers using protein embeddings as features
  • Developers building high-throughput inference pipelines on Forge/Biohub
  • Teams integrating ESM3/ESMC into internal or reproducibility pipelines

Examples

  1. "Design a GFP-like fluorescent protein with chain-of-thought" → produces staged structure → sequence → function generation code.
  2. "Embed 2,000 FASTA sequences with ESMC and cluster them" → suggests a batched LogitsConfig(return_embeddings=True) loop plus caching.
  3. "Inverse-fold target.pdb into 10 candidate sequences" → writes a script using ESMProtein.from_pdb() with temperature sweeps for diversity.

· · · Install guide · · ·

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/esm folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/esm/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/sas && mkdir -p ~/.claude/skills && cp -r /tmp/sas/skills/esm ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Create the skills directory: mkdir -p ~/.claude/skills
  3. Copy just this skill: cp -r scientific-agent-skills/skills/esm ~/.claude/skills/
  4. Verify that ~/.claude/skills/esm/SKILL.md and the references/ folder came along.
  5. Set up a Python 3.12 environment (required): uv venv --python 3.12 && uv pip install "esm==3.2.3"
  6. For hosted models, create an API key in the Biohub/Forge developer console and export it: export ESM_API_KEY=your_key (never hardcode it).
  7. Restart Claude Code and ask something like "write ESM3 code to generate a protein sequence" to trigger the skill.
View source on GitHub ↗License: MIT