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pubchem mcp server

pubchem mcp server

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github.com/sssjiangScience & Education11Updated 37w ago
Repository

About pubchem mcp server

pubchem mcp server retrieves basic chemical information about drugs from the PubChem API. It is intended for MCP clients that need drug identifiers and molecular properties.

Key features

  1. 01PubChem API drug lookups
  2. 02CAS number retrieval
  3. 03Molecular formula and weight
  4. 04SMILES and synonyms

Use cases

  1. 01Retrieve chemical details for a named drug
  2. 02Find CAS numbers and molecular properties

MCP support

Exposes drug chemical information retrieved from the PubChem API to MCP clients.

#pubchem#mcp#drug-information

Configuration

Local server config is the same for every client. Copy it into your client’s MCP config file.

mcp.json · Universal config
{
  "mcpServers": {
    "pubchem_mcp_server": {
      "command": "uvx",
      "args": [
        "pubchem_mcp_server"
      ]
    }
  }
}
Run commanduvx pubchem_mcp_server

Local servers need a runtime on your machine (e.g. Node.js 18+). Config file locations differ by client; see your client’s docs.

Packages
pypipubchem_mcp_server

Tools

No tool list yet

Local servers expose tools only once running on your machine, and the maintainer has not provided a tool list.

Details

From the project README

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"
}

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