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ChEMBL MCP Server

A comprehensive Model Context Protocol (MCP) server providing advanced access to the ChEMBL chemical database.

Installation

Add the following to your MCP client configuration file.

Configuration

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

The ChEMBL MCP Server provides programmatic access to the ChEMBL chemical database through a Model Context Protocol (MCP) server. It exposes a comprehensive suite of tools for chemical data retrieval, target analysis, bioactivity data, drug development insights, chemical property analysis, and advanced search capabilities, all designed to power AI assistants and MCP clients in drug discovery workflows.

How to use

You run the MCP server locally or via a container and connect your MCP client to it to perform tasks such as compound lookups, target queries, bioactivity exploration, and more. When you start the server, it communicates over standard input/output (stdio) so your MCP client can send requests and receive responses in real time. You can also run the server inside Docker and connect through the same MCP client interface.

How to install

# Prerequisites
- Node.js v16 or higher
- npm (or yarn)

# Local installation (build and run)
git clone <repository-url>
cd chembl-server
npm install
npm run build
npm start
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Available tools

search_compounds

Search the ChEMBL database by compound name, synonym, or identifier.

get_compound_info

Retrieve detailed information for a specific compound by ChEMBL ID.

search_by_inchi

Find compounds by InChI key or InChI string.

get_compound_structure

Retrieve chemical structure information in formats like SMILES, InChI, MOL, or SDF.

search_similar_compounds

Identify chemically similar compounds using Tanimoto similarity.

search_targets

Search for biological targets by name or type.

get_target_info

Retrieve detailed target information and annotations.

get_target_compounds

Get compounds tested against a specific target.

search_by_uniprot

Find ChEMBL targets by UniProt accession numbers.

get_target_pathways

List biological pathways associated with targets.

search_activities

Search bioactivity measurements and assay results.

get_assay_info

Retrieve detailed assay information and conditions.

search_by_activity_type

Find bioactivity data by activity type and value range.

get_dose_response

Obtain dose-response data and activity profiles.

compare_activities

Compare bioactivity data across multiple compounds or targets.

search_drugs

Search for approved drugs and clinical candidates.

get_drug_info

Retrieve 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.

analyze_admet_properties

Analyze ADMET properties (Absorption, Distribution, Metabolism, Excretion, Toxicity).

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 and related metrics.

substructure_search

Find compounds containing specific substructures.

batch_compound_lookup

Process multiple ChEMBL IDs efficiently.

get_external_references

Provide links to external databases (PubChem, DrugBank, PDB, etc.).

advanced_search

Perform complex queries with multiple chemical and biological filters.