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alphafold-skill

Submit compact AlphaFold Protein Structure Database API requests for prediction, UniProt summary, sequence summary, and annotation lookups. Use when a user wants AlphaFold metadata or concise structure summaries

Stars
1,305
Source
openai/plugins
Updated
2026-05-30
Slug
openai--plugins--alphafold-skill
View on GitHubRaw SKILL.md

// install — copy + paste into any project

mkdir -p .claude/skills && curl -fsSL https://raw.githubusercontent.com/openai/plugins/HEAD/plugins/life-science-research/skills/alphafold-skill/SKILL.md -o .claude/skills/alphafold-skill.md

Drops the SKILL.md into .claude/skills/alphafold-skill.md. Works with Claude Code, Cursor, and any agent that loads SKILL.md files from .claude/skills/.

Operating rules

  • Use scripts/rest_request.py for all AlphaFold API calls.
  • Use base_url=https://alphafold.ebi.ac.uk/api.
  • The script accepts max_items, but set it explicitly only when trimming array-heavy responses; single-entry lookups usually do not need it.
  • For sequence/summary or annotations, start around max_items=3 to 5.
  • Re-run the request if the conversation is long instead of trusting older tool output.
  • Treat displayed ... in tool previews as UI truncation, not part of the real request.
  • If the user asks for full JSON, set save_raw=true and report the saved file path instead of pasting the payload into chat.

Execution behavior

  • Return concise markdown summaries from the script JSON by default.
  • Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
  • Prefer these paths: prediction/<qualifier>, uniprot/summary/<qualifier>.json, sequence/summary, and annotations/<qualifier>.json.
  • Keep sequence-style inputs compact and prefer rerunning instead of copying prior output back into context.

Input

  • Read one JSON object from stdin.
  • Required fields: base_url, path
  • Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
  • Common AlphaFold patterns:
    • {"base_url":"https://alphafold.ebi.ac.uk/api","path":"prediction/Q5VSL9"}
    • {"base_url":"https://alphafold.ebi.ac.uk/api","path":"uniprot/summary/Q5VSL9.json"}
    • {"base_url":"https://alphafold.ebi.ac.uk/api","path":"annotations/Q5VSL9.json","params":{"type":"MUTAGEN"},"max_items":3}

Output

  • Success returns ok, source, path, method, status_code, warnings, and either compact records or a compact summary.
  • Use raw_output_path when save_raw=true.
  • Failure returns ok=false with error.code such as invalid_json, invalid_input, network_error, or invalid_response.

Execution

echo '{"base_url":"https://alphafold.ebi.ac.uk/api","path":"prediction/Q5VSL9"}' | python scripts/rest_request.py

References

  • No additional runtime references are required; keep the import package limited to this file and scripts/rest_request.py.