pubchem-mcp-server
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PubChem MCP Server is a Model Context Protocol server designed to provide AI models with access to chemical compound data from the PubChem database. It offers querying capabilities by name or CID, retrieves detailed compound properties, and supports various data output formats.
PubChem MCP Server
A Model Context Protocol (MCP) server for retrieving chemical compound data from PubChem database.
Features
- Query compounds by name or PubChem CID
- Retrieve comprehensive compound data including IUPAC name, molecular formula, molecular weight, SMILES notation, InChI, and InChIKey
- Support for multiple output formats: JSON, CSV, XYZ
- Built-in caching system to improve performance
- Automatic retry mechanism for API reliability
- Fallback 3D structure generation if PubChem 3D is unavailable
Requirements
- Python 3.8+
- Requests library
- RDKit (optional)
Available Tools
get_pubchem_data
- Retrieves chemical compound structure and property data.
download_structure
- Downloads structure files for a compound.