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ChEMBL MCP Server

@BioMCP-Hub

Repository

Basic information

Category

Other

Transports

stdio

Author

BioMCP-Hub

About ChEMBL MCP Server

No overview available yet

#chembl#api#database

ChEMBL MCP Server config

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

{
  "mcpServers": {
    "chembl-mcp-server-biomcp-hub": {
      "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?

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

How to use ChEMBL-MCP-Server?

Clone the repository, install dependencies with pip install -r requirements.txt, then start the server using python chembl_searver.py. Configure it via command-line parameters such as --host, --port, --transport (http or stdio), and --log-level.

Key features of ChEMBL-MCP-Server

  • 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
  • Data entity APIs (activity, assay, target, molecule, drug, and more)
  • Chemical tool APIs (SMILES canonicalization, conversion, structural alerts)

Use cases of ChEMBL-MCP-Server

  • Retrieving activity, assay, target, molecule, or drug data from ChEMBL
  • Canonicalizing SMILES strings or converting SMILES to InChI/SVG
  • Querying structural alerts for chemical compounds
  • Integrating ChEMBL data into MCP-compatible workflows

Frequently asked questions

1

What does the ChEMBL-MCP-Server do?

It wraps the ChEMBL web resource client into a FastMCP server for asynchronous API access.

2

How do I install the server?

Clone the repository and run `pip install -r requirements.txt`.

3

How do I start the server?

Run `python chembl_searver.py` with optional parameters like `--host`, `--port`, `--transport`, and `--log-level`.

4

What transport methods are supported?

HTTP and stdio transports are supported. Default is HTTP.

5

What dependencies are required?

The server requires chembl_webresource_client, mcp, fastapi, uvicorn, and asyncio.

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