ChEMBL-MCP-Server

ChEMBL-MCP-Server

By JackKuo666 GitHub

🔍 Enable AI assistants to search, access, and analyze ChEMBL through a simple MCP interface.

Overview

what is ChEMBL-MCP-Server?

ChEMBL-MCP-Server is a bioinformatics tool designed to provide access to the ChEMBL database, which contains information on bioactive drug-like small molecules.

how to use ChEMBL-MCP-Server?

To use ChEMBL-MCP-Server, visit the GitHub repository and follow the installation instructions to set up the server. Once running, you can query the database for chemical and biological data.

key features of ChEMBL-MCP-Server?

  • Access to a comprehensive database of bioactive compounds
  • Ability to perform complex queries on chemical and biological data
  • Integration with various bioinformatics tools for data analysis

use cases of ChEMBL-MCP-Server?

  1. Researchers can find information on drug candidates and their biological activities.
  2. Chemists can analyze chemical properties and structures of compounds.
  3. Bioinformaticians can integrate ChEMBL data into their workflows for drug discovery.

FAQ from ChEMBL-MCP-Server?

  • What kind of data can I access with ChEMBL-MCP-Server?

You can access data on bioactive compounds, including their chemical structures, biological activities, and pharmacological properties.

  • Is ChEMBL-MCP-Server free to use?

Yes! ChEMBL-MCP-Server is open-source and free for everyone to use.

  • How can I contribute to ChEMBL-MCP-Server?

You can contribute by reporting issues, suggesting features, or submitting pull requests on the GitHub repository.

Content

ChEMBL-MCP-Server

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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

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

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