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ChEMBL MCP Server

@JackKuo666

Repository

Basic information

Category

Other

Transports

stdio

Author

JackKuo666

About ChEMBL MCP Server

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

ChEMBL MCP Server config

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

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

ChEMBL MCP Server tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

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

Frequently asked questions

1

What dependencies does ChEMBL-MCP-Server require?

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

2

How do I start the server with the stdio transport?

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

3

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).

4

Are there example scripts?

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

5

What license is ChEMBL-MCP-Server distributed under?

It is licensed under the MIT License.

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