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Pubchem MCP Server

PubChem MCP Server is a bridge service that connects AI assistants with the PubChem chemical database through the Model Context Protocol (MCP), providing functions such as compound search, structure acquisition, and property query.
Research and dataEducation and learning tools#Chemical search#Compound query#Molecular structure#Chemical data.Python
2 points
7.4K
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Overview

Installation

Content Details

Alternatives

What is PubChem MCP Server?

PubChem MCP Server is a bridge tool that connects AI assistants with the PubChem chemical database. It allows users to query chemical compounds and obtain detailed information through a simple interface without the need for professional chemical knowledge.

How to use PubChem MCP Server?

Simply install the server and send a query request through the AI assistant to obtain information such as the name, structure, and properties of chemical compounds. It supports multiple installation methods and clients.

Applicable scenarios

Suitable for scenarios such as chemical research, drug development, and education that require quick access to compound information. Especially suitable for non - chemistry professionals to quickly query chemical data.

Main functions

Compound search
Supports querying compounds by name, SMILES code, or CID
Chemical structure
Obtain molecular structure and identifier information
Physical property data
Retrieve detailed chemical and physical property data
Advanced search
Supports precise queries with multiple parameter combinations
Molecular visualization
Generate and display molecular structures (under development)
Advantages
Simplify the chemical data query process without the need for professional chemical knowledge
Support multiple query methods (name, SMILES, CID, etc.)
Compatible with multiple AI clients (Claude, Cursor, etc.)
Provide detailed physical property data of compounds
Limitations
Some advanced functions are still under development
Requires an internet connection to access the PubChem database
Query results depend on the accuracy of the PubChem database

How to use

Install the server
Choose a method suitable for your client to install PubChem MCP Server
Start the server
Run the server program
Send a query request
Send a compound query request through the AI client

Usage examples

Query common drug information
Query the basic information and chemical properties of aspirin
Query by SMILES code
Use the SMILES code to query specific compounds
Get detailed physical property data
Get detailed physical property data of a compound by CID

Frequently asked questions

How to obtain the CID of a compound?
Which clients are supported?
What if the query results are inaccurate?

Related resources

PubChem official website
Official website of the PubChem chemical database
GitHub repository
Project source code and latest updates
Smithery platform
MCP server hosting platform

Installation

Copy the following command to your Client for configuration
{
  "mcpServers": {
    "pubchem": {
      "command": "python",
      "args": ["-m", "pubchem-mcp-server"]
      }
  }
}

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

{
  "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": []
    }
  }
}
Note: Your key is sensitive information, do not share it with anyone.

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