Agent skill · research science · google-deepmind
pubchem-database
Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.
Why this skill is useful
Adds a Python wrapper script for querying the PubChem database, enabling complex cheminformatics tasks that the AI cannot perform without it.
What it needs
Requires uv installed locally. About 3k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
PubChem Database Prerequisites 1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH. 2. User Notification: If .licenses/pubchemdatabaseLICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://pubchem.ncbi.nlm.nih.gov/docs/citation-guidelines and https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest, then (2) create the file recording the notification text and timestamp. Quick Start PubChem queries are executed via a robust Python wrapper script to respect terms-of-service and handle complex JSON parsing. This script allows safe multi-agent use of APIs. Example: Resolve a chemical name to its Compound ID (CID) Core Rules Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully. Read the generated JSON output file, and process it with jq or code. Verify Facts: ALWAYS verify information retrieved from memory with a database query if the user asks for a specific fact that can be checked in PubChem. Do not rely solely on internal knowledge. Notification: If this skill is used, ensure this is mentioned in the output. Core Capabilities 1. Compound Resolution (Name or InChI to Identifiers) Convert chemical/trade names or InChI strings into PubChem CIDs, SMILES, and InChIKeys. 2. Physical & Chemical Property Retrieval Fetch computed properties (e.g., MolecularWeight, XLogP, TPSA). 3. Synonyms and Trade Names Find alternative names and brand names. Advanced Context 4. Safety and Hazard Information (GHS) Retrieve Global Harmonized System hazard statements and handling precautions (uses PUG-View). 5. Drug and Medication Information Fetch FDA pharmacology data, mechanism of action, and therapeutic uses (uses PUG-View). 6. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/pubchem_database