ChEMBL MCP Server

Chembl mcp server lets Claude, Cursor and other MCP clients work with ChEMBL directly. A comprehensive Model Context Protocol server for accessing ChEMBL chemical database with 27 specialized tools for drug discovery, chemical informatics, and bioactivity analysis.

What ChEMBL does

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.

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.

Tools it exposes

Once connected, the assistant can call these 7 tools directly:

• InChI — based Search**: Find compounds by InChI key or InChI string
• Dose — Response Analysis**: Get dose-response data and activity profiles
• Drug — Likeness Assessment**: Assess drug-likeness using Lipinski Rule of Five and other metrics
• User-Agent — ChEMBL-MCP-Server/1.0.0
• Timeout — 30 seconds
• Prerequisites — The Prerequisites tool exposed by this server
• Setup — The Setup tool exposed by this server

Installing the chembl mcp server

Setup follows the standard MCP pattern: clone or install the server, then register it in your client's configuration file and restart the client. The configuration snippets on this page cover Claude Desktop, Claude Code and Cursor.

Requirements

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

Where it fits

Database servers turn schema archaeology and ad-hoc reporting into conversation, which is why they tend to be the second or third server people install. ChEMBL sits in that group, and the shape of its toolset — InChI, Dose, Drug among others — tells you what it is really for. Worth comparing against the other databases servers in this directory before you commit to one, since several overlap in scope but differ sharply in setup cost and permissions.

Practical notes

• This server runs locally, so it operates with whatever access your machine and its credentials already have. Scope that deliberately rather than by default.
• With 7 tools exposed, expect a noticeable bump in prompt size — disable it in projects that never use ChEMBL.
• Maintained by Augmented-Nature, written in TypeScript.
• MCP clients ask for confirmation before each tool call by default. Keep that on while you learn what the chembl mcp server actually does with your data.
• Every entry in this directory is reviewed by hand before it goes live, and details are checked against the project's own documentation.