PubChem-MCP-Server
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The PubChem MCP Server provides a bridge between AI assistants and PubChem's chemical database through the Model Context Protocol (MCP).
PubChem MCP Server
๐งช 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.
๐ค Contribute โข ๐ Report Bug
โจ Core Features
- ๐ Compound Search: Query PubChem compounds by name, SMILES, or CID โ
- ๐งช Chemical Structure: Access molecular structures and identifiers โ
- ๐ Property Data: Retrieve detailed chemical and physical properties โ
- ๐ฌ Advanced Search: Combine multiple parameters for precise queries โ
- ๐งฌ Molecular Visualization: Generate and display molecular structures ๐
- ๐ Property Analysis: Compare properties across multiple compounds ๐
- ๐๏ธ Local Storage: Save frequently used compounds for faster access ๐
- ๐ Chemistry Prompts: Specialized prompts for chemical analysis ๐
๐ 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 โ Cursor Settings โ MCP โ 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
๐ 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.
๐ 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 compoundmax_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 compoundmax_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 compoundsmiles
(str, optional): SMILES notation of the chemical compoundformula
(str, optional): Molecular formulacid
(int, optional): PubChem Compound IDmax_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:
โข Compound name
โข CID (PubChem Compound ID)
โข Molecular formula
โข 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:
โข IUPAC name
โข Molecular formula
โข Molecular weight
โข SMILES notation
โข InChI and InChIKey
โข Physical and chemical properties
โข Synonyms
๐ 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.
๐ 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
๐ Project Structure
pubchem_server.py
: The main MCP server implementation using FastMCPpubchem_search.py
: Contains example code for searching PubChem
๐ง 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
๐ค Contributing
Contributions are welcome! Please feel free to submit a Pull Request.
๐ License
This project is licensed under the MIT License.
โ ๏ธ Disclaimer
This tool is for research purposes only. Please respect PubChem's terms of service and use this tool responsibly.