How do I use PubChem-MCP?

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type @ followed by the MCP server name and your instructions, e.g., "@PubChem-MCP What are the molecular properties and CID for Ibuprofen?" That's it! The server will respond to your query, and you can continue using it as needed. Here is a step-by-step guide with screenshots.

PubChem-MCP

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.

Features

Search for compounds by name, structure, or identifier
Retrieve detailed information about compounds and substances
Access bioassay data and molecular properties
Query chemical classifications and cross-references
Compatible with any MCP client, including Claude for Desktop

Installation

Option 1: From GitHub

# Clone the repository git clone https://github.com/BioContext/PubChem-MCP.git cd PubChem-MCP # Create a virtual environment uv venv source .venv/bin/activate # On Windows: .venv\Scripts\activate # Install dependencies pip install -r requirements.txt

Option 2: Using pip (Once published)

pip install pubchem-mcp

Usage

Running as a standalone server

# From source python -m mcp_server # If installed via pip pubchem-mcp

Using with Claude for Desktop

Install Claude for Desktop
Configure Claude for Desktop to use this server by editing ~/Library/Application Support/Claude/claude_desktop_config.json (macOS/Linux) or %AppData%\Claude\claude_desktop_config.json (Windows):

{ "mcpServers": { "pubchem": { "command": "python", "args": [ "-m", "mcp_server" ] } } }

Restart Claude for Desktop
You can now use the PubChem tools in Claude

Example queries for Claude

"Find information about aspirin in PubChem"
"What are the properties of compound CID 2244?"
"Show me the structure of paracetamol"

Available Tools

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
And more...

Development

# Clone the repository git clone https://github.com/BioContext/PubChem-MCP.git cd PubChem-MCP # Create a virtual environment uv venv source .venv/bin/activate # On Windows: .venv\Scripts\activate # Install development dependencies pip install -e ".[dev]" # Run tests pytest