Chembl MCP Server

A ChEMBL database API access service based on the FastMCP framework, providing support for asynchronous calls and multiple transport methods.

Research and data Developer tools #ChEMBL interface #Asynchronous service #Chemical database #API encapsulation .Python

rating : 2 points

downloads : 4.7K

update time : 2025-04-23

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What is ChEMBL-MCP-Server?

ChEMBL-MCP-Server is an API service based on the FastMCP framework. It encapsulates the chemical and biological activity data of the ChEMBL database, providing a convenient query interface for researchers. Through this service, users can easily obtain key data such as drug molecules, biological targets, and activity tests.

How to use ChEMBL-MCP-Server?

You can access the ChEMBL database through simple API calls without complex configuration. The service supports two interaction methods: HTTP and standard input/output, which are suitable for integration requirements in different scenarios.

Applicable scenarios

It is suitable for scenarios such as drug discovery research, chemoinformatics analysis, and biological activity data mining. Researchers can quickly obtain the required chemical data through the API to accelerate the research process.

Main features

Full ChEMBL data access

Provides API access to all entities (molecules, targets, activity data, etc.) in the ChEMBL database

Asynchronous API calls

High-performance asynchronous API implemented based on the FastMCP framework, supporting concurrent request processing

Built-in error handling

Automated error handling and timeout mechanism to ensure service stability

Multiple transport methods

Supports two transport methods, HTTP and stdio, to meet different integration requirements

Chemical tools API

Provides practical chemical tools such as SMILES standardization and structure conversion

Advantages

Simplifies the access process of the ChEMBL database

High-performance asynchronous API design

Perfect error handling mechanism

Supports multiple transport protocols

Rich chemical data processing tools

Limitations

Requires an Internet connection to access the ChEMBL database

There may be performance limitations for large-scale data queries

Requires basic knowledge of API calls

How to use

Install the service

Clone the code repository and install the dependencies

Start the service

Choose a suitable startup method

Call the API

Call the API interface through an HTTP client or command-line tool

Usage cases

Query molecule activity data

Obtain all biological activity test results of a specific molecule in ChEMBL

SMILES standardization

Convert the SMILES string of a chemical molecule into a standard form

Obtain the SVG image of a molecule

Convert the molecular structure into an SVG format image

Frequently Asked Questions

Do I need a ChEMBL account to use it?

What should I do if there is a delay in the query results?

How can I obtain the latest chemical data?

Which chemical format conversions are supported?

Related resources

ChEMBL official website

The official website of the ChEMBL database

GitHub code repository

Project source code and latest updates

FastMCP framework documentation

Technical documentation of the underlying framework

Chemoinformatics tutorial

An introductory tutorial on chemoinformatics

🚀 ChEMBL-MCP-Server

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

✨ Features

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

📦 Installation

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

# Install dependencies
pip install -r requirements.txt

💻 Usage Examples

Basic Usage

Start the server

# Start the HTTP server with default configuration
python chembl_searver.py

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

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

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

Available parameters

--host: Server host address, default is 127.0.0.1.
--port: Server port, default is 8000.
--transport: Transmission method, optional values are http or stdio, default is http.
--log-level: Log level, optional values are DEBUG, INFO, WARNING, ERROR, CRITICAL, default is INFO.