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" }