PubChem MCP Server

🧪 Enable AI assistants to search and access chemical compound information through a simple MCP interface.

The PubChem MCP Server provides a bridge between AI assistants and PubChem's chemical database through the Model Context Protocol (MCP). It allows AI models to search for chemical compounds and access their detailed information in a programmatic way.

🤝 Contribute • 📝 Report Bug

✨ Core Features

• 🔎 Compound Search: Query PubChem compounds by name, SMILES, or CID ✅
• 🧪 Chemical Structure: Access molecular structures and identifiers ✅
• 📊 Property Data: Retrieve detailed chemical and physical properties ✅
• 🔬 Advanced Search: Combine multiple parameters for precise queries ✅
• 🧬 Molecular Visualization: Generate and display molecular structures 📝
• 📈 Property Analysis: Compare properties across multiple compounds 📝
• 🗃️ Local Storage: Save frequently used compounds for faster access 📝
• 📝 Chemistry Prompts: Specialized prompts for chemical analysis 📝

🚀 Quick Start

Installing via Smithery

To install PubChem Server for Claude Desktop automatically via Smithery:

Claude

npx -y @smithery/cli@latest install @JackKuo666/pubchem-mcp-server --client claude --config "{}"

Cursor

Paste the following into Settings → Cursor Settings → MCP → Add new server:

• Mac/Linux

npx -y @smithery/cli@latest run @JackKuo666/pubchem-mcp-server --client cursor --config "{}" 

Windsurf

npx -y @smithery/cli@latest install @JackKuo666/pubchem-mcp-server --client windsurf --config "{}"

CLine

npx -y @smithery/cli@latest install @JackKuo666/pubchem-mcp-server --client cline --config "{}"

Installing Manually

Install using uv:

uv tool install pubchem-mcp-server

For development:

# Clone and set up development environment
git clone https://github.com/JackKuo666/PubChem-MCP-Server.git
cd PubChem-MCP-Server

# Create and activate virtual environment
uv venv
source .venv/bin/activate
uv pip install -r requirements.txt

📊 Usage

Start the MCP server:

python pubchem_server.py

Once the server is running, you can use the provided MCP tools in your AI assistant or application. Here are some examples of how to use the tools:

Example 1: Search for compounds by name

result = await mcp.use_tool("search_pubchem_by_name", {
    "name": "aspirin",
    "max_results": 3
})
print(result)

Example 2: Search for compounds by SMILES notation

result = await mcp.use_tool("search_pubchem_by_smiles", {
    "smiles": "CC(=O)OC1=CC=CC=C1C(=O)O",  # Aspirin's SMILES
    "max_results": 2
})
print(result)

Example 3: Get detailed information for a specific compound

result = await mcp.use_tool("get_pubchem_compound_by_cid", {
    "cid": 2244  # Aspirin's CID
})
print(result)

Example 4: Perform an advanced search with multiple parameters

result = await mcp.use_tool("search_pubchem_advanced", {
    "name": "caffeine",
    "formula": "C8H10N4O2",
    "max_results": 2
})
print(result)

These examples demonstrate how to use the four main tools provided by the PubChem MCP Server. Adjust the parameters as needed for your specific use case.

🛠 MCP Tools

The PubChem MCP Server provides the following tools:

search_pubchem_by_name

Search for chemical compounds on PubChem using a compound name.

Parameters:

• name (str): Name of the chemical compound
• max_results (int, optional): Maximum number of results to return (default: 5)

Returns: List of dictionaries containing compound information

search_pubchem_by_smiles

Search for chemical compounds on PubChem using a SMILES string.

Parameters:

• smiles (str): SMILES notation of the chemical compound
• max_results (int, optional): Maximum number of results to return (default: 5)

Returns: List of dictionaries containing compound information

get_pubchem_compound_by_cid

Fetch detailed information about a chemical compound using its PubChem CID.

Parameters:

• cid (int): PubChem Compound ID (CID)

Returns: Dictionary containing compound information

search_pubchem_advanced

Perform an advanced search for compounds on PubChem.

Parameters:

• name (str, optional): Name of the chemical compound
• smiles (str, optional): SMILES notation of the chemical compound
• formula (str, optional): Molecular formula
• cid (int, optional): PubChem Compound ID
• max_results (int, optional): Maximum number of results to return (default: 5)

Returns: List of dictionaries containing compound information

Usage with Claude Desktop

Add this configuration to your claude_desktop_config.json:

(Mac OS)

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

(Windows version):

{
  "mcpServers": {
    "pubchem": {
      "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe",
      "args": [
        "-m",
        "pubchem-mcp-server"
      ]
    }
  }
}

Using with Cline

{
  "mcpServers": {
    "pubchem": {
      "command": "bash",
      "args": [
        "-c",
        "source /home/YOUR/PATH/mcp-hub/PubChem-MCP-Server/.venv/bin/activate && python /home/YOUR/PATH/mcp-hub/PubChem-MCP-Server/pubchem_server.py"
      ],
      "env": {},
      "disabled": false,
      "autoApprove": []
    }
  }
}

After restarting Claude Desktop, the following capabilities will be available:

Searching Compounds

You can ask Claude to search for chemical compounds using queries like:

Can you search PubChem for information about aspirin?

The search will return basic information about matching compounds including:

• Compound name

• CID (PubChem Compound ID)

• Molecular formula

• Molecular weight

Getting Compound Details

Once you have a CID, you can ask for more details:

Can you show me the details for compound with CID 2244?

This will return:

• IUPAC name

• Molecular formula

• Molecular weight

• SMILES notation

• InChI and InChIKey

• Physical and chemical properties

• Synonyms

📝 TODO

visualize_compound

Generate and display a 2D or 3D visualization of a chemical compound.

compare_compounds

Compare properties and structures of multiple compounds.

save_compound

Save a compound locally for faster access.

list_saved_compounds

List all saved compounds.

📝 Chemistry Prompts

The server will offer specialized prompts to help analyze chemical compounds:

Compound Analysis Prompt

A comprehensive workflow for analyzing chemical compounds that only requires a compound ID:

result = await call_prompt("deep-compound-analysis", {
    "compound_id": "2244"
})

This prompt will include:

• Detailed instructions for using available tools
• A systematic workflow for compound analysis
• Comprehensive analysis structure covering:
  • Chemical structure and properties
  • Pharmacological properties
  • Biological activities
  • Applications and uses
  • Safety and toxicity information
  • Related compounds

📁 Project Structure

• pubchem_server.py: The main MCP server implementation using FastMCP
• pubchem_search.py: Contains example code for searching PubChem

🔧 Dependencies

• Python 3.10+
• FastMCP
• asyncio
• logging
• pubchempy (for PubChem API access)
• pandas (for data handling)

You can install the required dependencies using:

pip install mcp pubchempy pandas

🤝 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

📄 License

This project is licensed under the MIT License.

⚠️ Disclaimer

This tool is for research purposes only. Please respect PubChem's terms of service and use this tool responsibly.