What is the PubChem MCP Server used for?

The PubChem MCP Server enables AI-driven drug discovery and analysis by providing structured access to PubChem's chemical database, allowing you to retrieve and process detailed chemical information about drugs for research or analysis applications.

How do I install the PubChem MCP Server?

Clone the repository, navigate to the project directory, and run `pip install .` to install the dependencies.

How is the PubChem MCP Server configured?

Configuration is done via `servers_config.json` by specifying the server name as "pubchem" with the command "uvx" and args ["pubchem_mcp_server"].

What chemical information does the PubChem MCP Server return?

The server returns comprehensive drug details including drug name, CAS number, molecular weight, molecular formula, SMILES notation, synonyms, InChI Key, IUPAC name, ATC code, and a link to the full PubChem entry.

MCP Connector

Query PubChem for Drug Data

Name: PubChem MCP Server
Availability: OnlineOnly
Author: sssjiang

PubChem MCP Server extracts drug basic chemical information from the PubChem API, providing structured data like molecular formula and synonyms.

Connect

Works with pubchem

sssjiang

Maintainer?

Spark score

out of 100

Updated 5 months ago

Version 1.0.0

Models

universal

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Why it matters

Access comprehensive molecular and chemical data for drugs directly from the PubChem API. Retrieve essential information like formulas, weights, identifiers, and synonyms to enrich your research or applications.

Outcomes

What it gets done

Fetch drug CAS numbers and molecular weights

Retrieve molecular formulas and SMILES notation

Get drug synonyms, alternative names, and IUPAC names

Access InChI keys and ATC codes for classification

Install

Add it to your toolbox

Run in your project directory:

curl -fsSL https://spark.entire.vc/get/vb-pubchem | bash

Capabilities

Tools your agent gets

get_drug_information

Retrieve basic chemical information about drugs from PubChem API including formulas, weights, and identifiers.

get_cas_number

Obtain CAS numbers for chemical compounds from PubChem.

get_molecular_weight

Get molecular weights of drugs and chemical compounds.

get_molecular_formula

Retrieve molecular formulas for chemical compounds.

get_smiles_notation

Get SMILES notation for chemical structures.

get_drug_synonyms

Retrieve drug synonyms and alternative names from PubChem.

get_inchi_key

Access InChI keys for chemical compound identification.

get_iupac_name

Obtain IUPAC names for chemical compounds.

+2 tools

Overview

PubChem MCP Server

The PubChem MCP Server is a connector designed to extract basic chemical information about drugs from the PubChem API. It provides structured data points such as the drug name, CAS number, molecular weight, molecular formula, SMILES string, synonyms, InChI Key, IUPAC name, ATC code, and a direct link to the details on PubChem. This tool should be used when an AI client needs to access and process fundamental chemical properties of drugs available in the PubChem database. It is suitable for applications requiring structured chemical data for research, analysis, or integration into larger workflows.

What it does

As an AI client, I want to easily access and process detailed chemical information about drugs from PubChem, so that I can integrate this data into my applications for research or analysis.

The big job is to enable AI-driven drug discovery and analysis by providing structured access to PubChem's vast chemical database.

The small job is to retrieve specific chemical properties for a given drug, formatted in a machine-readable way.

Installation involves cloning the repository and installing dependencies:

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

Configuration for the MCP server is done via servers_config.json:

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

The output provides comprehensive drug details:

{
  "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"
}

Source 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"
}

FAQ

Common questions

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