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skill CX Codex GP ChatGPT official · OpenAI

bindingdb-skill — Codex skill: BindingDB lookups

This skill queries BindingDB for ligand-target data by PDB, UniProt, or molecular similarity. Use it when you need a concise result summary or a saved raw response.

Install into Codex · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add openai/plugins --skill bindingdb-skill -a codex
Open on GitHub

What bindingdb-skill does

The skill runs scripts/rest_request.py to query BindingDB. It supports ligand lookups by PDB, UniProt, and SMILES, plus target searches by compound. By default, the agent returns a concise Markdown summary; it can save the full response to a file when asked.

The script reads one JSON object from standard input. Set the API path and request parameters there; response=application/json requests structured output. For saving the complete response, use save_raw and raw_output_path. Some empty-result responses may have an empty body, so there may be no records to summarize.

For broad lookups, the skill recommends starting with max_items=10; similarity searches are better with 5-10. In a long conversation, run the request again instead of relying on an earlier tool result.

What it helps with

  • look up ligands by PDB identifier
  • find ligands associated with a UniProt protein
  • search for compounds similar to a SMILES string
  • retrieve targets for a compound
  • save the full BindingDB response to a file

Example prompts for the agent

  • Look up ligands for PDB 1Q0L and summarize the results.
  • Find ligands for this UniProt entry and return a concise summary.
  • Search for compounds similar to this SMILES and save the full response.

How to install bindingdb-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill bindingdb-skill -a codex

2Manually: put the files in place

.agents/skills/bindingdb-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about bindingdb-skill

How do I install bindingdb-skill in Codex?

Run npx skills add openai/plugins --skill bindingdb-skill. The skill will then be available in Codex.

What does bindingdb-skill do?

It queries BindingDB for ligands by PDB, UniProt, or SMILES, and for targets by compound. Results are returned as a concise summary by default.

How does similarity search work?

Provide a SMILES string and request parameters. The skill recommends setting max_items to 5-10; use save_raw and raw_output_path to save the complete response.

See also

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