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

Clone the repository:

git clone <repository-url>
cd chembl-server

Install dependencies:

npm install

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:

npm start

Adding to MCP Client Configuration

Add the server to your MCP client configuration (e.g., Claude Desktop):

{
  "mcpServers": {
    "chembl": {
      "command": "node",
      "args": ["/path/to/chembl-server/build/index.js"],
      "env": {}
    }
  }
}

Available Tools

1. search_compounds

Search the ChEMBL database for compounds by name, synonym, or identifier.

Parameters:

query (required): Search query (compound name, synonym, or identifier)
limit (optional): Number of results to return (1-1000, default: 25)
offset (optional): Number of results to skip (default: 0)

Example:

{
  "query": "aspirin",
  "limit": 10
}

2. get_compound_info

Get detailed information for a specific compound by ChEMBL ID.

Parameters:

chembl_id (required): ChEMBL compound ID (e.g., CHEMBL25)

Example:

{
  "chembl_id": "CHEMBL25"
}

3. search_targets

Search for biological targets by name or type.

Parameters:

query (required): Target name or search query
target_type (optional): Target type filter (e.g., SINGLE PROTEIN, PROTEIN COMPLEX)
organism (optional): Organism filter
limit (optional): Number of results to return (1-1000, default: 25)

Example:

{
  "query": "dopamine receptor",
  "organism": "Homo sapiens",
  "limit": 5
}

4. search_activities

Search bioactivity measurements and assay results.

Parameters:

target_chembl_id (optional): ChEMBL target ID filter
assay_chembl_id (optional): ChEMBL assay ID filter
molecule_chembl_id (optional): ChEMBL compound ID filter
activity_type (optional): Activity type (e.g., IC50, Ki, EC50)
limit (optional): Number of results to return (1-1000, default: 25)

Example:

{
  "target_chembl_id": "CHEMBL2095173",
  "activity_type": "IC50",
  "limit": 50
}

5. batch_compound_lookup

Process multiple ChEMBL IDs efficiently.

Parameters:

chembl_ids (required): Array of ChEMBL compound IDs (1-50)

Example:

{
  "chembl_ids": ["CHEMBL25", "CHEMBL59", "CHEMBL1642"]
}

Resource Templates

The server provides direct access to ChEMBL data through URI templates:

1. Compound Information

URI: chembl://compound/{chembl_id}
Description: Complete compound information for a ChEMBL ID
Example: chembl://compound/CHEMBL25

2. Target Information

URI: chembl://target/{chembl_id}
Description: Complete target information for a ChEMBL target ID
Example: chembl://target/CHEMBL2095173

3. Assay Information

URI: chembl://assay/{chembl_id}
Description: Complete assay information for a ChEMBL assay ID
Example: chembl://assay/CHEMBL1217643

4. Activity Information

URI: chembl://activity/{activity_id}
Description: Bioactivity measurement data for an activity ID
Example: chembl://activity/12345678

5. Search Results

URI: chembl://search/{query}
Description: Search results for compounds matching the query
Example: chembl://search/aspirin

Examples

Basic Compound Search

Search for aspirin-related compounds:

// Tool call
{
  "tool": "search_compounds",
  "arguments": {
    "query": "aspirin",
    "limit": 5
  }
}

Get Detailed Compound Information

Retrieve comprehensive information about aspirin:

// Tool call
{
  "tool": "get_compound_info",
  "arguments": {
    "chembl_id": "CHEMBL25"
  }
}

Target-based Search

Find compounds tested against dopamine receptors:

// Tool call
{
  "tool": "search_targets",
  "arguments": {
    "query": "dopamine receptor D2",
    "organism": "Homo sapiens"
  }
}

Bioactivity Analysis

Search for IC50 data against a specific target:

// Tool call
{
  "tool": "search_activities",
  "arguments": {
    "target_chembl_id": "CHEMBL2095173",
    "activity_type": "IC50",
    "limit": 100
  }
}

Batch Processing

Process multiple compounds efficiently:

// Tool call
{
  "tool": "batch_compound_lookup",
  "arguments": {
    "chembl_ids": ["CHEMBL25", "CHEMBL59", "CHEMBL1642", "CHEMBL1201585"]
  }
}

API Integration

This server integrates with the ChEMBL REST API for programmatic access to chemical data. For more information about ChEMBL:

ChEMBL Website: https://www.ebi.ac.uk/chembl/
API Documentation: https://chembl.gitbook.io/chembl-interface-documentation/web-services
REST API Guide: https://www.ebi.ac.uk/chembl/api/data/docs

All API requests include:

User-Agent: ChEMBL-MCP-Server/1.0.0
Timeout: 30 seconds
Base URL: https://www.ebi.ac.uk/chembl/api/data

Error Handling

The server includes comprehensive error handling:

Input Validation: All parameters are validated using type guards
API Errors: Network and API errors are caught and returned with descriptive messages
Timeout Handling: Requests timeout after 30 seconds
Graceful Degradation: Partial failures are handled appropriately

Development

Build the Project

npm run build

Development Mode

Run TypeScript compiler in watch mode:

npm run dev

Project Structure

chembl-server/
├── src/
│   └── index.ts          # Main server implementation
├── build/                # Compiled JavaScript output
├── package.json          # Node.js dependencies and scripts
├── tsconfig.json         # TypeScript configuration
└── README.md            # This file

Dependencies

@modelcontextprotocol/sdk: Core MCP SDK for server implementation
axios: HTTP client for ChEMBL API requests
typescript: TypeScript compiler for development

License

MIT License

Contributing

Fork the repository
Create a feature branch
Make your changes
Add tests if applicable
Submit a pull request

Support

For issues and questions:

Check the ChEMBL API documentation
Review the Model Context Protocol specification
Open an issue on the repository

About Augmented Nature

This comprehensive ChEMBL MCP Server is developed by Augmented Nature, a leading innovator in AI-powered bioinformatics and computational chemistry solutions. Augmented Nature specializes in creating advanced tools that bridge the gap between artificial intelligence and chemical research, enabling researchers to unlock deeper insights from chemical and biological data.

Complete Tool Reference

Core Chemical Search & Retrieval Tools

search_compounds - Search ChEMBL database by name, synonym, or identifier
get_compound_info - Get detailed compound information by ChEMBL ID
search_by_inchi - Find compounds by InChI key or InChI string
get_compound_structure - Retrieve chemical structures in various formats
search_similar_compounds - Find chemically similar compounds using Tanimoto similarity

Target Analysis & Drug Discovery Tools

search_targets - Search for biological targets by name or type
get_target_info - Get detailed target information by ChEMBL target ID
get_target_compounds - Get compounds tested against specific targets
search_by_uniprot - Find ChEMBL targets by UniProt accession
get_target_pathways - Get biological pathways associated with targets

Bioactivity & Assay Data Tools

search_activities - Search bioactivity measurements and assay results
get_assay_info - Get detailed assay information by ChEMBL assay ID
search_by_activity_type - Find bioactivity data by activity type and value range
get_dose_response - Get dose-response data and activity profiles
compare_activities - Compare bioactivity data across multiple compounds

Drug Development & Clinical Data Tools

search_drugs - Search for approved drugs and clinical candidates
get_drug_info - Get drug development status and clinical trial information
search_drug_indications - Search for therapeutic indications and disease areas
get_mechanism_of_action - Get mechanism of action and target interaction data

Chemical Property Analysis Tools

analyze_admet_properties - Analyze ADMET properties
calculate_descriptors - Calculate molecular descriptors and physicochemical properties
predict_solubility - Predict aqueous solubility and permeability properties
assess_drug_likeness - Assess drug-likeness using Lipinski Rule of Five

Advanced Search & Cross-Reference Tools

substructure_search - Find compounds containing specific substructures
batch_compound_lookup - Process multiple ChEMBL IDs efficiently
get_external_references - Get links to external databases
advanced_search - Complex queries with multiple chemical and biological filters

Changelog

v1.0.0 - Initial Release

Comprehensive Chemical Intelligence: 27 specialized tools for drug discovery
Core Functionality: Compound search, target analysis, bioactivity data
Advanced Features: Similarity search, batch processing, cross-references
Resource Templates: Direct URI-based access to ChEMBL data
Docker Support: Containerized deployment with security best practices
Professional Documentation: Complete tool reference and examples
Developed by Augmented Nature: Professional chemical informatics platform

This server cannot be installed

security - not tested

license - permissive license

quality - not tested

ChEMBL MCP Server

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