pubchem-compound-search
PubChem Compound Search
Overview
PubChem is the world's largest freely available chemical database with 110M+ compounds. This skill covers searching compounds by name, structure, or identifier, retrieving molecular properties, performing similarity/substructure searches, and accessing bioactivity data through PubChemPy (Python wrapper) and PUG-REST API (direct HTTP).
When to Use
- Looking up a compound by name, CAS number, or SMILES to get its PubChem CID and properties
- Retrieving molecular properties (molecular weight, LogP, TPSA, H-bond counts) for known compounds
- Finding structurally similar compounds via Tanimoto similarity search
- Searching for compounds containing a specific substructure (pharmacophore screening)
- Converting between chemical identifier formats (name ↔ CID ↔ SMILES ↔ InChI)
- Accessing bioactivity screening data (assay results, active/inactive status)
- Batch property comparison across a set of drug candidates
- For local molecular computation (fingerprints, descriptors, 3D conformers), use
rdkitinstead - For querying multiple databases (UniProt, KEGG, ChEMBL) in one workflow, use
bioservicesinstead
Prerequisites
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