Unofficial ChEMBL MCP Server

A comprehensive Model Context Protocol (MCP) server providing advanced access to the ChEMBL chemical database. This server offers 22 specialized tools enabling AI assistants and MCP clients to perform sophisticated drug discovery research, chemical informatics analysis, and bioactivity investigations directly through ChEMBL's REST API.

Developed by Augmented Nature

Features

Core Chemical Search & Retrieval (5 tools)

• Compound Search: Search the ChEMBL database by compound name, synonym, or identifier
• Detailed Compound Info: Retrieve comprehensive compound information including structure, properties, and annotations
• InChI-based Search: Find compounds by InChI key or InChI string
• Structure Retrieval: Get chemical structure information in various formats (SMILES, InChI, MOL, SDF)
• Similarity Search: Find chemically similar compounds using Tanimoto similarity

Target Analysis & Drug Discovery (5 tools)

• Target Search: Search for biological targets by name or type
• Detailed Target Info: Retrieve comprehensive target information and annotations
• Target Compounds: Get compounds tested against specific targets
• UniProt Integration: Find ChEMBL targets by UniProt accession numbers
• Target Pathways: Associated biological pathways and mechanisms

Bioactivity & Assay Data (5 tools)

• Activity Search: Search bioactivity measurements and assay results
• Detailed Assay Info: Get comprehensive assay protocols and conditions
• Activity Type Search: Find bioactivity data by specific activity type and value range
• Dose-Response Analysis: Get dose-response data and activity profiles
• Activity Comparison: Compare bioactivity data across multiple compounds or targets

Drug Development & Clinical Data (4 tools)

• Drug Search: Search for approved drugs and clinical candidates
• Drug Development Status: Get drug development status and clinical trial information
• Therapeutic Indications: Search for therapeutic indications and disease areas
• Mechanism of Action: Get mechanism of action and target interaction data

Chemical Property Analysis (4 tools)

• ADMET Analysis: Analyze ADMET properties (Absorption, Distribution, Metabolism, Excretion, Toxicity)
• Molecular Descriptors: Calculate molecular descriptors and physicochemical properties
• Solubility Prediction: Predict aqueous solubility and permeability properties
• Drug-Likeness Assessment: Assess drug-likeness using Lipinski Rule of Five and other metrics

Advanced Search & Cross-References (4 tools)

• Substructure Search: Find compounds containing specific substructures
• Batch Processing: Process multiple ChEMBL IDs efficiently
• External References: Get links to external databases (PubChem, DrugBank, PDB, etc.)
• Advanced Search: Complex queries with multiple chemical and biological filters

Resource Templates

• Direct access to ChEMBL data via URI templates for seamless integration

Installation

Prerequisites

• Node.js (v16 or higher)
• npm or yarn

Setup

1. Clone the repository:

git clone <repository-url>
cd chembl-server

2. Install dependencies:

npm install

3. Build the project:

npm run build

Docker

Building the Docker Image

Build the Docker image:

docker build -t chembl-mcp-server .

Running with Docker

Run the container:

docker run -i chembl-mcp-server

For MCP client integration, you can use the container directly:

{
  "mcpServers": {
    "chembl": {
      "command": "docker",
      "args": ["run", "-i", "chembl-mcp-server"],
      "env": {}
    }
  }
}

Usage

As an MCP Server

The server is designed to run as an MCP server that communicates via stdio:

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... [View full README on GitHub](https://github.com/Augmented-Nature/ChEMBL-MCP-Server#readme)