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Molecule

Verified Integration
Author: @ChatMol•Category: ServerApplication
GitHub Repository
JSON-RPC 2.0
Protocol Standard
Sub-second
Execution Latency
Active
Operational Status
Tags:#Claude#Search#Database#API#Git#AI#GitHub#Node.js

Client Configuration

— Connect Molecule to Claude Desktop or Cursor in seconds
{
  "mcpServers": {
    "molecule": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-molecule"
      ],
      "env": {}
    }
  }
}
Paste into ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows).
Architecture & Capabilities

System Overview

Connects molecular science tools to Claude AI for prompt-assisted molecule modeling and co-scientific interaction.

Indexed Date

7/23/2026

License

Open Source

Protocol Layer

stdio / SSE RPC

Frequently Asked Questions

Architecture and operational details for Molecule

You need to have Claude Desktop installed and running. You also need to install mcp and have access to molecular science tools like PyMOL or ChimeraX.

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