ChEMBL-MCP-Server

@JackKuo666

About ChEMBL-MCP-Server

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

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "ChEMBL-MCP-Server": {
      "command": "python",
      "args": [
        "chembl_searver.py"
      ]
    }
  }
}

Tools

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Overview

What is ChEMBL-MCP-Server?

ChEMBL-MCP-Server is a FastMCP wrapper server based on the chembl_webresource_client package that provides complete API access to the ChEMBL database. It is designed for researchers and developers who need programmatic access to drug discovery data and chemical tools.

How to use ChEMBL-MCP-Server?

Install dependencies with pip install -r requirements.txt, then start the server by running python chembl_searver.py. You can configure the host, port, transport method, and log level using command-line arguments such as --host, --port, --transport, and --log-level.

Key features of ChEMBL-MCP-Server

Complete API access to the ChEMBL database
Asynchronous API calls using the FastMCP framework
Built-in error handling and timeout mechanisms
Support for both HTTP and stdio transport methods
Full type annotations and docstrings

Use cases of ChEMBL-MCP-Server

Query activity, assay, target, molecule, and drug data from ChEMBL
Canonicalize SMILES strings or convert SMILES to InChI and SVG images
Retrieve structural alerts for chemical compounds
Integrate ChEMBL data retrieval into MCP-based workflows
Serve as a backend for drug discovery and cheminformatics tools

FAQ from ChEMBL-MCP-Server

What dependencies does ChEMBL-MCP-Server require?

It requires chembl_webresource_client, mcp, fastapi, uvicorn, and asyncio.

How do I start the server with the stdio transport?

Run python chembl_searver.py --transport stdio to use stdio transport instead of HTTP.

What API functions are available?

The server provides data entity APIs (activity, assay, target, molecule, drug) and chemical tool APIs (canonicalize SMILES, SMILES to InChI, SMILES to SVG, structural alerts).

Are there example scripts?

Yes, check the chembl_search.py file for examples of using the various APIs.

What license is ChEMBL-MCP-Server distributed under?

It is licensed under the MIT License.

Frequently asked questions

What dependencies does ChEMBL-MCP-Server require?

It requires chembl_webresource_client, mcp, fastapi, uvicorn, and asyncio.

How do I start the server with the stdio transport?

Run `python chembl_searver.py --transport stdio` to use stdio transport instead of HTTP.

What API functions are available?

The server provides data entity APIs (activity, assay, target, molecule, drug) and chemical tool APIs (canonicalize SMILES, SMILES to InChI, SMILES to SVG, structural alerts).

Are there example scripts?

Yes, check the `chembl_search.py` file for examples of using the various APIs.

What license is ChEMBL-MCP-Server distributed under?

It is licensed under the MIT License.

Comments

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