Agent skill · research science · aiskillstore
pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
Why this skill is useful
Provides specific commands and patterns for querying and retrieving data from the PubChem database that the AI wouldn't reliably generate on its own.
What it needs
Requires pandas, pubchempy installed locally. About 7k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
PubChem Database Overview PubChem is the world's largest freely available chemical database with 110M+ compounds and 270M+ bioactivities. Query chemical structures by name, CID, or SMILES, retrieve molecular properties, perform similarity and substructure searches, access bioactivity data using PUG-REST API and PubChemPy. When to Use This Skill This skill should be used when: Searching for chemical compounds by name, structure (SMILES/InChI), or molecular formula Retrieving molecular properties (MW, LogP, TPSA, hydrogen bonding descriptors) Performing similarity searches to find structurally related compounds Conducting substructure searches for specific chemical motifs Accessing bioactivity data from screening assays Converting between chemical identifier formats (CID, SMILES, InChI) Batch processing multiple compounds for drug-likeness screening or property analysis Core Capabilities 1. Chemical Structure Search Search for compounds using multiple identifier types: By Chemical Name: By CID (Compound ID): By SMILES: By InChI: By Molecular Formula: 2. Property Retrieval Retrieve molecular properties for compounds using either high-level or low-level approaches: Using PubChemPy (Recommended): Get Specific Properties: Batch Property Retrieval: Available Properties: MolecularFormula, MolecularWeight, CanonicalSMILES, IsomericSMILES, InChI, InChIKey, IUPACName, XLogP, TPSA, HBondDonorCount, HBondAcceptorCount, RotatableBondCount, Complexity, Charge, and many more (see references/apireference.md for complete list). 3. Similarity Search Find structurally similar compounds using Tanimoto similarity: Note: Similarity searches are asynchronous for large queries and may take 15-30 seconds to complete. PubChemPy handles the asynchronous pattern automatically. 4. Substructure Search Find compounds containing a specific structural motif: Common Substructures: Benzene ring: c1ccccc1 Pyridine: c1ccncc1 Phenol: c1ccc(O)cc1 Carboxylic acid: C(=O)O 5. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/pubchem-database