PubChem MCP Server
by JackKuo666
The PubChem MCP Server bridges AI assistants and PubChem's chemical database through the Model Context Protocol (MCP). It enables AI models to search for chemical compounds and access their detailed information programmatically.
Last updated: N/A
What is PubChem MCP Server?
The PubChem MCP Server is a tool that allows AI assistants to search and access chemical compound information from the PubChem database using a simple Model Context Protocol (MCP) interface.
How to use PubChem MCP Server?
Install the server using Smithery or manually using uv. Start the server using python pubchem_server.py. Then, use the provided MCP tools in your AI assistant or application, sending requests with appropriate parameters (e.g., compound name, SMILES, CID) to the server. Refer to the examples provided in the README for specific tool usage.
Key features of PubChem MCP Server
Compound Search
Chemical Structure Access
Property Data Retrieval
Advanced Search
Molecular Visualization (TODO)
Property Analysis (TODO)
Local Storage (TODO)
Chemistry Prompts (TODO)
Use cases of PubChem MCP Server
Searching for chemical compounds by name or SMILES
Retrieving detailed information about a specific compound
Performing advanced searches with multiple parameters
Integrating chemical information into AI workflows
Analyzing chemical compounds using specialized prompts
FAQ from PubChem MCP Server
What is MCP?
What is MCP?
MCP stands for Model Context Protocol. It's a protocol for AI models to interact with external tools and services.
How do I install the server?
How do I install the server?
You can install the server using Smithery or manually using uv. Refer to the README for detailed instructions.
What dependencies are required?
What dependencies are required?
Python 3.10+, FastMCP, asyncio, logging, pubchempy, and pandas are required. You can install them using pip install mcp pubchempy pandas.
How do I search for a compound by name?
How do I search for a compound by name?
Use the search_pubchem_by_name tool with the name parameter set to the compound name.
How do I get detailed information about a compound?
How do I get detailed information about a compound?
Use the get_pubchem_compound_by_cid tool with the cid parameter set to the PubChem Compound ID.