Epitope Prediction (bioSkills)

A Claude Code skill that identifies antibody-binding (B-cell) and MHC-presented (T-cell) immunogenic regions of an antigen for vaccine design and epitope mapping.

   
Type Claude Skill
Supplier GPTomics bioSkills (community OSS, MIT)
Availability GA — part of the bioSkills collection
Pricing Free / OSS (MIT)
Capabilities Read/Write — Claude runs the skill’s workflow locally (Bash/Python), not as an MCP tool
Verified works · 2026-07-20
Security cleared · 2026-07-20 — provenance matches GPTomics/bioSkills, MIT, no advisories, read-only local epitope workflow

How to install

bioSkills is not an npm package — skills are plain markdown/code read directly by the agent. Clone the repo, then either run the installer for the whole category or copy the single skill directory.

  • Claude Code — clone and install via the bundled script: 
    git clone https://github.com/GPTomics/bioSkills
cd bioSkills
./install-claude.sh --categories "immunoinformatics"

    The installer copies matching skills into ~/.claude/skills/ (default target). Use ./install-claude.sh --list to preview and --dry-run to see what would be copied.

  • Claude Code / other agents — copy just this one skill: 
    cp -r bioSkills/immunoinformatics/epitope-prediction ~/.claude/skills/

    (run from inside your clone — the previous step left you in bioSkills/; otherwise replace bioSkills/ with the absolute path of your clone). The skill declares its external dependencies (BepiPred-3.0, DiscoTope-3.0, NetMHCpan/MHCflurry) in SKILL.md; install them when prompted on first use.

What it does

Scores candidate epitopes across the two arms of adaptive immunity:

  • B-cell (antibody) epitopes — BepiPred-3.0 for linear sequence-based scoring and DiscoTope-3.0 for structure-based conformational prediction (the more defensible route when a 3D model/AlphaFold structure exists).
  • T-cell epitopes — MHC class I presentation via NetMHCpan-4.1 / MHCflurry and class II / integrated CTL prediction via NetMHCIIpan / NetCTLpan, with an IEDB REST API wrapper for multiple predictors.

The skill is explicit that T-cell prediction is mature (AUC > 0.9) while sequence-only B-cell prediction is unreliable because ~90% of real epitopes are conformational — steering the user to structure-based methods for B-cell work.

Primary use cases: vaccine antigen selection, epitope mapping, cross-strain epitope conservation checks.

Notes

Distributed as a SKILL.md (plus reference material) in the bioSkills collection — Claude executes the workflow locally via Bash/Python rather than as an MCP server. The upstream skill front-matter name is bio-immunoinformatics-epitope-prediction; if you invoke it as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /epitope-prediction. NetMHCpan and some IEDB standalone tools require a separate (free, academic) download/registration from their vendors. Upstream directory: immunoinformatics/epitope-prediction.

Sources

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