MertAtesmen/pubchem-mcp

PubChem MCP Server

This mcp server allows AI Agents to retrieve chemical data using the PUG View and PUG Rest API.

Main Idea Behind the Development of the Project

The main problem with other PubChem Tools and PubChem MCP Servers is the fact that they retrieve only the fraction of the information PubChem offers. This MCP server uses the classic PUG Rest API for retrieving the standard information from the API. But it also retrieves rich information from the PUG View API using Text Extraction Methods.

Notes

• Currently the MCP server only retrieves a small subset of Compound data from Pubchem.

Prerequisites

• git installed. (To clone the repo)
• uv installed.
• docker installed (Optional: If you are planning to use the SSE server inside a docker container).

To install uv in Linux and MacOS type this in your terminal:

curl -LsSf https://astral.sh/uv/install.sh | sh

Running the SSE server

While inside the repo run:

uv run pubchem-mcp-sse

Running on STDIO

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "command": "uv",
      "args": [
        "run",
        "--directory",
        "<LOCATION-TO-THE-REPO>",
        "pubchem-mcp-stdio"
      ]
    }
  }
}

Docker SSE Server

First you need to build the image using the Dockerfile inside this repository. Run this to build the image:

docker build -t pubchem-mcp .

Then you can run the container using this command:

docker run --name pubchem-mcp \
  -p 127.0.0.1:8000:8000 \
  pubchem-mcp