pubchem-mcp-server

pubchem-mcp-server

3.3
research_and_datadatabases

If you are the rightful owner of pubchem-mcp-server and would like to certify it and/or have it hosted online, please leave a comment on the right or send an email to henry@mcphub.com.

A Model Context Protocol (MCP) server for retrieving chemical compound data from PubChem database.

PubChem MCP Server is a Python implementation of an MCP server that allows AI models to query chemical compound information from the PubChem database. It provides easy access to compound properties, 2D structures, and 3D molecular coordinates through a standard MCP interface.

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 (default), CSV, XYZ (3D structure)
  • Built-in caching system to improve performance
  • Automatic retry mechanism for API reliability

Tools

  1. get_pubchem_data

    Retrieves chemical compound structure and property data.

  2. download_structure

    Downloads structure files for a compound.

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