getcompanion-ai/fair-esm2
skills/fair-esm2/SKILL.md
Use ESM2 protein language models for embeddings, mutation scoring, remote homology, or representation analysis. Use when a task needs protein embeddings, zero-shot variant scores, clustering, or sequence-function triage.
$ install --global
skillsauthnpx skillsauth add getcompanion-ai/feynman fair-esm2Install this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- fair-esm2
- description:
- Use ESM2 protein language models for embeddings, mutation scoring, remote homology, or representation analysis. Use when a task needs protein embeddings, zero-shot variant scores, clustering, or sequence-function triage.
Fair ESM2
Use this skill for ESM2-style protein language model analysis.
Workflow:
- Normalize proteins into FASTA with stable identifiers and mutation notation.
- Verify the local package, checkpoint, endpoint, or notebook route before execution.
- Save embeddings, variant-score tables, clustering plots, model version, command, and runtime logs.
- Compare model-derived rankings against UniProt, structures, conservation, assays, or literature.
- Mark sequence regions with poor coverage, disorder, low homology, or domain-boundary ambiguity.
Use ESM2 outputs as features or hypotheses unless a source-backed validation step supports the conclusion.
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