pubchem-database - Query PubChem compounds and bioactivity data
Queries PubChem for compounds, molecular properties, structure searches, identifiers, bioactivity data, annotations, and structure files.
Tags
Updated: 2026-10-01Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Search compounds by identifiers
- Retrieve molecular properties
- Perform similarity searches
- Perform substructure searches
- Convert chemical formats
- Download structure files
- Generate structure images
- Retrieve compound synonyms
- Query bioactivity data
- Retrieve compound annotations
- Process compound batches
Inputs
- Chemical names
- PubChem CIDs
- SMILES strings
- InChI strings
- Molecular formulas
- Similarity thresholds
- Substructure patterns
- Bioassay IDs
- Biological target names
- Output filenames
Outputs
- Compound search results
- Molecular property records
- Similarity search matches
- Substructure search matches
- Chemical identifiers
- Synonym lists
- Bioactivity records
- Compound annotations
- Structure files
- Structure images
- Batch analysis results
Requirements
- Python environment
- Internet access to PubChem
- pubchempy package
- requests package for direct API access
- pandas package for optional analysis