PubChem MCP Server

Example Use Cases

• 1

  Search PubChem for compounds by name, structure (SMILES/InChI), or identifier (CID) and retrieve matching results.

• 2

  Detailed compound information and properties (physical/chemical) programmatically for downstream analysis or reporting.

• 3

  Access bioassay records, substance details, classifications, and cross-references from PubChem within an MCP-compatible workflow.

Description

PubChem-MCP is a Model Context Protocol (MCP) server that provides tools for querying the PubChem database for compounds, substances, bioassays, and related information. It supports searching compounds by name, structure, or identifier and retrieving detailed compound properties, bioassay data, classifications, and cross-references. The server can run locally or be installed via pip and is designed to integrate with MCP clients (including Claude for Desktop). It is useful for chemical informatics workflows and agents that need programmatic access to molecular data.