MyChem MCP Server

A Model Context Protocol (MCP) server that provides access to the MyChem API.

Features

Core Capabilities

• Chemical Search: Search by name, formula, InChI, SMILES, CAS, or molecular properties (MW, LogP, HBD/HBA)
• Drug Information: Access data from DrugBank, ChEMBL, PubChem, and PharmGKB
• Structure Operations: Convert between formats, search by structure, calculate properties
• Identifier Mapping: Convert between PubChem CID, ChEMBL ID, DrugBank ID, and 6 other ID types
• Batch Processing: Query up to 1000 chemicals in a single request
• Bioactivity Data: Search compounds by target activity, compare bioassays across molecules
• ADMET Properties: Retrieve absorption, distribution, metabolism, excretion, and toxicity data
• Clinical Data: Access clinical trials, FDA approval status, and regulatory information
• Biological Context: Explore pathways, disease associations, and mechanisms of action
• Patent Information: Search patent data and intellectual property landscape
• Data Export: Export results in TSV, CSV, JSON, SDF, or Markdown formats

Data Sources

• PubChem: Chemical structures, properties, bioassays
• ChEMBL: Bioactive molecules, drug discovery data
• DrugBank: Comprehensive drug information, interactions, targets
• PharmGKB: Pharmacogenomics data
• FDA: Approval status and label information
• Patent databases: Chemical patent information
• Clinical trials: Drug development pipeline data

Prerequisites

• Python 3.12+ with pip

Quick Start

1. Install UV

UV is a fast Python package and project manager.

pip install uv

2. Install MCPM (MCP Manager)

MCPM is a package manager for MCP servers that simplifies installation and configuration.

pip install mcpm

3. Setup the MCP Server

cd mychem-mcp
uv sync

4. Add the Server to Claude Desktop

# Make sure you're in the project directory
cd mychem-mcp

# Set Claude as the target client
mcpm target set @claude-desktop

# Add the MyChem MCP server
mcpm import stdio mychem \
  --command "$(uv run which python)" \
  --args "-m mychem_mcp.server"

Then restart Claude Desktop.

Usage

Running the Server

uv run python -m mychem_mcp.server

Development

uv run pytest tests/ -v