How do I use PubChem MCP Server?

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type @ followed by the MCP server name and your instructions, e.g., "@PubChem MCP Server Get the molecular formula and SMILES for Caffeine" That's it! The server will respond to your query, and you can continue using it as needed. Here is a step-by-step guide with screenshots.

pubchem mcp server

the mcp is used to extract the drug basic chemical infomation from pubchem API.

Requirements

Python 3.10
python-dotenv
requests
mcp
uvicorn

Installation

Install the dependencies(local):

Install directly from the project directory

git clone [project repository URL]
cd [project directory]
pip install .

Configure servers(pypi):

The servers_config.json follows the same structure as Claude Desktop, allowing for easy integration of multiple servers. Here's an example:

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

the result of this MCP

{
  "Drug Name": "Aspirin",
  "CAS Number": "50-78-2",
  "Molecular Weight": 180.16,
  "Molecular Formula": "C9H8O4",
  "SMILES": "CC(=O)OC1=CC=CC=C1C(=O)O",
  "Synonyms": [
    "2-(Acetyloxy)benzoic Acid",
    "Acetylsalicylic Acid",
    "Acetysal",
    "Acylpyrin",
    "Aloxiprimum",
    "Aspirin",
    "Colfarit",
    "Dispril",
    "Easprin"
  ],
  "InchI Key": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
  "IUPAC Name": "2-acetyloxybenzoic acid",
  "ATC Code": "N02BA01",
  "Details Link": "https://pubchem.ncbi.nlm.nih.gov/compound/2244"
}