Koskamo

PubChem Finder MCP

PubChem Finder is an MCP server that enables molecular similarity and substructure searches over PubChem using a local fingerprint index. It provides offline chemistry capabilities via RDKit, including descriptors, standardization, alerts, and structure drawings. It also wraps PubChem's live services to retrieve names, safety data, GHS classifications, pharmacology, toxicity, and bioassay summaries without rate limits or timeouts associated with the web API.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

PubChem Finder MCP logo, by MysterionRiseCommunity listingLocal stdioSource reviewed; not executedPublished by MysterionRise
Vendor documentation

What you can do with it

  • Perform exact similarity and substructure searches over PubChem compounds
  • Retrieve molecular descriptors, QED, and synthetic accessibility scores
  • Check GHS labels and safety data for chemical hazards
  • Identify main targets of compounds in PubChem bioassays

Source and maintenance

Community listingRegistry 2.1.1
mcp-registry: io.github.MysterionRise/pubchem-finder@2.1.1Source repositoryProject website
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

pubchem-finder 2.1.1

pypiuvx
pubchem-finder package definition
{
  "version": "2.1.1",
  "transport": "stdio",
  "identifier": "pubchem-finder",
  "runtimeHint": "uvx",
  "registryType": "pypi",
  "registryBaseUrl": "https://pypi.org",
  "packageArguments": [
    {
      "type": "positional",
      "value": "mcp",
      "valueHint": "mcp"
    }
  ],
  "runtimeArguments": [
    {
      "name": "--python",
      "type": "named",
      "value": "3.14",
      "description": "Python 3.11-3.14: FPSim2, numexpr and ndindex publish no wheels for 3.15 yet"
    }
  ],
  "environmentVariables": [
    {
      "name": "PUBCHEM_FINDER_HOME",
      "format": "filepath",
      "description": "Data directory for the local index and the PubChem response cache (default: the platform's user data directory)"
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "pubchem-finder-mcp": {
      "command": "uvx",
      "args": [
        "pubchem-finder==2.1.1",
        "mcp"
      ],
      "env": {
        "PUBCHEM_FINDER_HOME": "<YOUR_PUBCHEM_FINDER_HOME>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "pubchem-finder-mcp": {
      "command": "uvx",
      "args": [
        "pubchem-finder==2.1.1",
        "mcp"
      ],
      "env": {
        "PUBCHEM_FINDER_HOME": "<YOUR_PUBCHEM_FINDER_HOME>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "pubchem-finder-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "pubchem-finder==2.1.1",
        "mcp"
      ],
      "env": {
        "PUBCHEM_FINDER_HOME": "<YOUR_PUBCHEM_FINDER_HOME>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "pubchem-finder-mcp": {
      "command": "uvx",
      "args": [
        "pubchem-finder==2.1.1",
        "mcp"
      ],
      "env": {
        "PUBCHEM_FINDER_HOME": "<YOUR_PUBCHEM_FINDER_HOME>"
      }
    }
  }
}

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