Search PubChem by structure: a local similarity/substructure index, live PubChem data, RDKit tools
Connect Runs on your machine
claude mcp add pubchem-finder -e PUBCHEM_FINDER_HOME=<PUBCHEM_FINDER_HOME> -- uvx pubchem-finder==2.2.2{
"mcpServers": {
"pubchem-finder": {
"command": "uvx",
"args": [
"pubchem-finder==2.2.2"
],
"env": {
"PUBCHEM_FINDER_HOME": "<PUBCHEM_FINDER_HOME>"
}
}
}
}{
"mcpServers": {
"pubchem-finder": {
"command": "uvx",
"args": [
"pubchem-finder==2.2.2"
],
"env": {
"PUBCHEM_FINDER_HOME": "<PUBCHEM_FINDER_HOME>"
}
}
}
}{
"servers": {
"pubchem-finder": {
"type": "stdio",
"command": "uvx",
"args": [
"pubchem-finder==2.2.2"
],
"env": {
"PUBCHEM_FINDER_HOME": "<PUBCHEM_FINDER_HOME>"
}
}
}
}Replace the values in angle brackets with your own. Keys stay on your machine; we never see them.
Tools
This server runs locally, so its tools are listed by your MCP client once it starts.
Environment variables
| Name | Description |
|---|---|
PUBCHEM_FINDER_HOMEOptional | Data directory for the local index and the PubChem response cache (default: the platform's user data directory) |
Details
| Package | [email protected] (PYPI, stdio) |
| First published | 11 Nov 2026 |
| Last updated | 11 Nov 2026 |
| Registry name | io.github.MysterionRise/pubchem-finder |
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