Description

This MCP server provides comprehensive access to the PubChem chemical database through 30 specialized tools covering compound search, structure analysis, property calculation, bioassay data, safety information, and cross-references to external databases. Built by Augmented Nature using TypeScript and the PubChem REST API, it enables chemical informatics workflows including similarity searches, ADMET prediction, drug-likeness assessment, toxicity analysis, and batch processing of up to 200 compounds. The implementation supports multiple search methods (name, SMILES, InChI, CAS numbers), provides detailed molecular descriptors and 3D conformer data, and integrates safety classifications with literature references, making it valuable for drug discovery, chemical research, regulatory compliance, and educational applications in chemistry and pharmacology.

Installation

git clone https://github.com/augmented-nature/pubchem-mcp-server

Claude Desktop Configuration

Add this configuration to your Claude Desktop config file to enable this MCP server:

Config file location: ~/Library/Application Support/Claude/claude_desktop_config.json

Config file location: %APPDATA%\Claude\claude_desktop_config.json

Config file location: ~/.config/Claude/claude_desktop_config.json

claude_desktop_config.json

{
  "mcpServers": {
    "pubchem": {
      "command": "node",
      "args": [
        "path/to/server.js"
      ]
    }
  }
}