Labsco
MCP SERVER

PubChem-MCP

by BioContext

Look up a compound's properties, the substance records behind it, and what it has been assayed against.

Physical Sciences & Scientific Computing
Summary
Chemistry lookups without the tab.

The three questions that actually come up — what is this compound, what are its numbers, what has it been tested against — answered in the thread that raised them rather than in a browser you then have to summarise from.

What it is

A Python MCP server over PubChem, covering compounds, substances and bioassays. It works with any MCP client, including Claude for Desktop, and needs no key.

What you get
  • Compounds searched by name or identifier
  • Detailed information for a compound
  • Physical and chemical properties for a compound
  • Bioassays searched
  • Detail for a substance record
Requirements

Python with uv: clone the repository, create the virtual environment and pip install -r requirements.txt, then run python -m mcp_server from your client config. No API key — PubChem's endpoints are public.

Setup effort

Build from source — clone the repository and build it, then point your client at the binary