An MCP (Model Context Protocol) server for accessing PubChem data. This server provides tools for querying the PubChem database for compounds, substances, bioassays, and related information.
pubchem-mcp is an MCP project maintained in the biocontext/pubchem-mcp repository. The maintainer describes its purpose as “An MCP (Model Context Protocol) server for accessing PubChem data. This server provides tools for querying the PubChem database for compounds, substances, bioassays, and related…”. Read the project documentation for the complete scope.
The project provides a local client configuration using python. Follow the repository’s build and installation steps before copying it, and replace example paths with the paths on your own computer.
Project documentation · Repository · Discovery listing. This profile records the public documentation checked on 2026-10-08.
Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.
| Tool | What it does |
|---|---|
| search_compound | Search for compounds by name or identifier |
| get_compound_details | Get detailed information about a compound |
| get_compound_properties | Get physical and chemical properties of a compound |
| search_bioassay | Search for bioassays |
| get_substance_details | Get detailed information about a substance |
{
"mcpServers": {
"pubchem": {
"command": "python",
"args": [
"-m",
"mcp_server"
]
}
}
}From the project documentation. Replace placeholders and example paths before connecting.
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