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bindingdb-skill

Submit compact BindingDB REST API requests for ligand-target binding lookups by PDB, UniProt, or similarity search. Use when a user wants concise BindingDB summaries; save raw payloads only on request.

Stars
1,305
Source
openai/plugins
Updated
2026-05-30
Slug
openai--plugins--bindingdb-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/bindingdb-skill/SKILL.md -o .claude/skills/bindingdb-skill.md

Drops the SKILL.md into .claude/skills/bindingdb-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 BindingDB API calls.
  • Use base_url=https://bindingdb.org.
  • Add response=application/json in params when you want structured output; some empty-result cases may still return an empty body.
  • For broad lookup endpoints, start around max_items=10; similarity-style queries are better with 5-10.
  • Re-run requests in long conversations instead of relying on older tool output.
  • Treat displayed ... in tool previews as UI truncation, not literal request content.

Execution behavior

  • Return concise markdown summaries from the script JSON by default.
  • Prefer these paths: rest/getLigandsByPDBs, rest/getLigandsByUniprots, rest/getLigandsBySmiles, and rest/getTargetsByCompound.
  • If the user needs the full payload, set save_raw=true and report the saved file path instead of pasting large response bodies into chat.

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 BindingDB patterns:
    • {"base_url":"https://bindingdb.org","path":"rest/getLigandsByPDBs","params":{"pdb":"1Q0L","cutoff":100,"identity":92,"response":"application/json"},"max_items":10}
    • {"base_url":"https://bindingdb.org","path":"rest/getLigandsBySmiles","params":{"smiles":"CC(=O)OC1=CC=CC=C1C(=O)O","cutoff":0.9,"response":"application/json"},"max_items":5}

Output

  • Success returns ok, source, path, method, status_code, warnings, and either compact records, a compact summary, or text_head.
  • Use raw_output_path when save_raw=true.
  • Failure returns ok=false with error.code and error.message.

Execution

echo '{"base_url":"https://bindingdb.org","path":"rest/getLigandsByPDBs","params":{"pdb":"1Q0L","cutoff":100,"identity":92,"response":"application/json"},"max_items":10}' | 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.