PubChem

Provides a PubChem-based MCP server to extract basic drug chemical information via API.

python

8

GitHub Stars

python

Language

6 months ago

First Indexed

2 months ago

Catalog Refreshed

Documentation & install

Readme and setup notes from the catalogue, plus a client-ready config you can copy for your MCP host.

Installation

Add the following to your MCP client configuration file.

Configuration

View docs

{
  "mcpServers": {
    "sssjiang-pubchem_mcp_server": {
      "command": "uvx",
      "args": [
        "pubchem_mcp_server"
      ]
    }
  }
}

You can run a PubChem-based MCP server that extracts basic drug chemical information from the PubChem API. This server enables MCP clients to query standardized drug data and receive structured results suitable for downstream tooling, analytics, or UI displays.

How to use

Run the local MCP server and connect your MCP client to it to retrieve drug information from PubChem. You can perform multiple queries to fetch fields such as Drug Name, CAS Number, Molecular Weight, Molecular Formula, and related identifiers. Use the client’s standard MCP request workflow to specify the drug you want and receive a structured response with key attributes like SMILES, InChI Key, IUPAC Name, ATC Code, and a detailed PubChem link.

How to install

Prerequisites: you need Python 3.10 or higher and the ability to install Python packages.

Step 1: Clone the project repository and navigate to the project directory.

git clone [project repository URL]
cd [project directory]

Step 2: Install the Python package and dependencies locally.

pip install .

Step 3: Configure the MCP server entry so your MCP client can discover and connect to it. Use the following configuration snippet to register the PubChem MCP server as a stdio connection.

{
  "mcpServers": {
    "pubchem": {
      "command": "uvx",
      "args": ["pubchem_mcp_server"]
    }
  }
}

Additional sections

Notes on running and security: the server is designed to be invoked locally via the uvx tool. Ensure you are running in a controlled environment and follow standard security practices for exposing MCP endpoints if you choose to run this in a shared or cloud environment.

Starting the server: after installation and configuration, you will typically start the MCP entry point using the configured stdio command. In this example, the command is provided as part of the local workflow.

Available tools

drug_info_extractor

Extracts basic chemical information for a drug by querying the PubChem API and returns structured fields such as Drug Name, CAS Number, Molecular Weight, Molecular Formula, SMILES, InChI Key, IUPAC Name, ATC Code, and a Details Link.