Bindingdb Skill

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.
• Every endpoint wraps its payload in a getLindsByUniprotResponse envelope (the getLinds spelling is BindingDB's, not a typo) whose records sit under the literal key bdb.affinities; reach them with record_path=getLindsByUniprotResponse.bdb.affinities.
• 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/getLigandsByUniprot, rest/getLigandsByUniprots, and rest/getTargetByCompound.
• 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/getTargetByCompound","params":{"smiles":"CC(=O)OC1=CC=CC=C1C(=O)O","cutoff":0.9,"response":"application/json"},"max_items":5,"record_path":"getLindsByUniprotResponse.bdb.affinities"}
  • {"base_url":"https://bindingdb.org","path":"rest/getLigandsByUniprot","params":{"uniprot":"P00734","response":"application/json"},"max_items":10,"record_path":"getLindsByUniprotResponse.bdb.affinities"}

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.