ChEMBL-MCP-Server

A FastMCP wrapper server based on the chembl_webresource_client package, providing API access to the ChEMBL database.

Features

• Complete API access to the ChEMBL database

• Asynchronous API calls implemented using FastMCP framework

• Built-in error handling and timeout mechanisms

• Support for both HTTP and stdio transport methods

• Complete type annotations and docstrings

Related MCP server: PubChem-MCP

Installation

# Clone repository
git clone https://github.com/yourusername/ChEMBL-MCP-Server.git
cd ChEMBL-MCP-Server

# Install dependencies
pip install -r requirements.txt

Usage

Starting the Server

# Start HTTP server with default configuration
python chembl_searver.py

# Specify host and port
python chembl_searver.py --host 0.0.0.0 --port 8080

# Use stdio transport
python chembl_searver.py --transport stdio

# Set log level
python chembl_searver.py --log-level DEBUG

Available Parameters

• --host: Server host address, defaults to 127.0.0.1

• --port: Server port, defaults to 8000

• --transport: Transport method, choose between http or stdio, defaults to http

• --log-level: Log level, choose from DEBUG, INFO, WARNING, ERROR, CRITICAL, defaults to INFO

API Functions

The server provides the following API functions:

Data Entity APIs

• example_activity: Get activity data

• example_assay: Get assay data

• example_target: Get target data

• example_molecule: Get molecule data

• example_drug: Get drug data

• More data entity APIs...

Chemical Tool APIs

• example_canonicalizeSmiles: Canonicalize SMILES strings

• example_smiles2inchi: Convert SMILES to InChI

• example_smiles2svg: Convert SMILES to SVG image

• example_structuralAlerts: Get structural alerts

• More chemical tool APIs...

Examples

Check the chembl_search.py file for examples of using various APIs.

Dependencies

• chembl_webresource_client: ChEMBL Web Service Client

• mcp: MCP Framework

• fastapi: FastAPI Framework

• uvicorn: ASGI Server

• asyncio: Asynchronous I/O Library

License

MIT