PubChem MCP Server
by PhelanShao
The PubChem MCP Server is a Python implementation of a Model Context Protocol (MCP) server designed to retrieve chemical compound data from the PubChem database. It provides easy access to compound properties, 2D structures, and 3D molecular coordinates through a standard MCP interface.
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What is PubChem MCP Server?
The PubChem MCP Server is a Python-based server that allows AI models to query chemical compound information from the PubChem database using the Model Context Protocol (MCP).
How to use PubChem MCP Server?
To use the server, you need to install it from source using pip. Then, configure your MCP configuration file to point to the server's mcp_server.py script. You can then use the available tools, get_pubchem_data and download_structure, by sending MCP requests with appropriate parameters like compound name/CID and desired output format.
Key features of PubChem MCP Server
Query compounds by name or PubChem CID
Retrieve comprehensive compound data (IUPAC name, molecular formula, weight, SMILES, InChI)
Support for JSON, CSV, and XYZ output formats
Built-in caching system for improved performance
Automatic retry mechanism for API reliability
Fallback 3D structure generation if PubChem 3D is unavailable
Use cases of PubChem MCP Server
Enabling AI models to understand and reason about chemical compounds
Integrating chemical data into AI-driven drug discovery pipelines
Providing AI models with access to chemical structures for property prediction
Using AI models to generate chemical structures based on desired properties
FAQ from PubChem MCP Server
What is MCP?
What is MCP?
MCP stands for Model Context Protocol, a standard for AI models to interact with external tools and servers.
What is PubChem?
What is PubChem?
PubChem is a public database of chemical molecules and their activities against biological assays.
How do I install the server?
How do I install the server?
Clone the repository, navigate to the python_version directory, and run pip install -e .
How do I configure the server for use with Claude?
How do I configure the server for use with Claude?
Add the provided JSON snippet to your MCP configuration file, adjusting the path to mcp_server.py as needed.
What output formats are supported?
What output formats are supported?
The server supports JSON, CSV, and XYZ output formats.