search_compoundLABSCO 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, then follow the project's own run instructions
USE CASES
01
Identifying a compound from a name
Search by name or identifier and get the right CID before anything else depends on it.
02
Getting the numbers for a calculation
Pull physical and chemical properties directly rather than copying them off a page.
03
Reading up on what a compound is
Get the full compound record, including classifications and cross-references.
04
Finding what a compound has been tested against
Search bioassays to see where it has already been screened.
05
Chasing a substance record back to its depositor
Read the substance entry behind a compound, which is where the source detail sits.
5 tools
Listed in project docs. Your client may show a different list.
get_compound_detailsget_compound_propertiessearch_bioassayget_substance_detailsBEFORE YOU INSTALL
What to know first
Tools you get
5 tools named in the project's documentation.
Requires
python on PATH
Where it runs
The documented client runs the server on your machine.
INSTALLATION
Connect your client
Server setup
TERMINAL
python -m mcp_serverMCP Clients
Claude Desktop
CLAUDE DESKTOP · JSON
{
"mcpServers": {
"pubchem": {
"command": "python",
"args": [
"-m",
"mcp_server"
]
}
}
}
