PubChem Database

Overview

PubChem is the world's largest freely available chemical database — 119M+ compounds, 322M+ substances, and 295M+ bioactivities per the PubChem 2025 update (Kim et al., NAR 2025). Query chemical structures by name, CID, or SMILES, retrieve molecular properties, perform similarity and substructure searches, and access bioactivity data using the 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