Unofficial PubChem MCP Server
A comprehensive Model Context Protocol (MCP) server for accessing the PubChem chemical database. This server provides access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools.
What is Unofficial PubChem MCP Server?
Unofficial PubChem MCP Server is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to comprehensive model context protocol (mcp) server for accessing the pubchem chemical database. this server provides access to over 110 million chemical compounds with extensive molecular properties, b...
A comprehensive Model Context Protocol (MCP) server for accessing the PubChem chemical database. This server provides access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools.
This server falls under the Data Science & ML category on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- A comprehensive Model Context Protocol (MCP) server for acce
Use Cases
Maintainer
Works with
Installation
Manual Installation
npx unofficial-pubchem-mcp-serverConfiguration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use Unofficial PubChem MCP Server
The Unofficial PubChem MCP Server provides comprehensive access to PubChem's database of over 110 million chemical compounds through 24 specialized tools. It enables researchers and chemists to search by name, SMILES, InChI, or CAS number; retrieve molecular properties and 3D conformers; analyze drug-likeness using Lipinski's rules; query bioassay data; assess safety and toxicity; and perform similarity and substructure searches — all through natural language in Claude without needing to write API calls.
Prerequisites
- Node.js 16+ and npm installed
- Internet access to the PubChem REST API (no API key required)
- An MCP-compatible client such as Claude Desktop or Claude Code
Clone the PubChem MCP Server repository
Download the server source code to your local machine.
git clone https://github.com/Augmented-Nature/PubChem-MCP-Server.git
cd PubChem-MCP-ServerInstall Node.js dependencies
Install the required npm packages.
cd pubchem-server
npm installBuild the server
Compile the server code.
npm run buildTest the server starts correctly
Run the server briefly to confirm it starts without errors before adding it to your MCP client.
npm startConfigure your MCP client
Add the server to claude_desktop_config.json. No API keys or environment variables are needed — PubChem's API is freely accessible. Note the rate limits: 5 requests/second, 400 requests/minute.
{
"mcpServers": {
"pubchem": {
"command": "node",
"args": ["/absolute/path/to/PubChem-MCP-Server/pubchem-server/dist/index.js"]
}
}
}Restart Claude Desktop and verify
Restart Claude Desktop and ask it to search for a common compound like aspirin to verify the 24 PubChem tools are available and working.
Unofficial PubChem MCP Server Examples
Client configuration
Example claude_desktop_config.json for the PubChem MCP Server — no API key needed.
{
"mcpServers": {
"pubchem": {
"command": "node",
"args": ["/Users/yourname/PubChem-MCP-Server/pubchem-server/dist/index.js"]
}
}
}Prompts to try
Example research prompts for the PubChem MCP Server.
- "Search PubChem for aspirin and give me its molecular formula, weight, and SMILES string"
- "Find compounds similar to ibuprofen with at least 85% structural similarity"
- "Check if the compound with CID 2244 (aspirin) satisfies Lipinski's Rule of Five for drug-likeness"
- "Get the 3D conformer data for caffeine"
- "Search for bioassays that tested compounds against the EGFR protein target"
- "Look up safety and toxicity information for acetaminophen"
- "Find all CAS registry numbers and synonyms for glucose"Troubleshooting Unofficial PubChem MCP Server
Rate limit errors from PubChem API
PubChem enforces a limit of 5 requests per second and 400 per minute. If you receive rate limit errors, space out your queries. The server respects these limits, but rapid sequential prompts may still trigger them. Wait a few seconds between complex multi-tool queries.
Compound not found for a search query
Try alternative search methods: if a name search fails, try searching by CAS number or SMILES string. PubChem's name matching is exact — try the IUPAC name or a common synonym. Use get_compound_synonyms to discover alternative names for a known compound.
Server exits immediately after 'npm start'
Ensure you ran 'npm run build' in the pubchem-server directory before starting. If the dist/ directory is missing, the build step has not completed. Check for build errors and ensure you are running Node.js 16+.
Frequently Asked Questions about Unofficial PubChem MCP Server
What is Unofficial PubChem MCP Server?
Unofficial PubChem MCP Server is a Model Context Protocol (MCP) server that comprehensive model context protocol (mcp) server for accessing the pubchem chemical database. this server provides access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools. It connects AI assistants to external tools and data sources through a standardized interface.
How do I install Unofficial PubChem MCP Server?
Follow the installation instructions on the Unofficial PubChem MCP Server GitHub repository. Clone the repo, install dependencies, and add the server config to your AI client.
Which AI clients work with Unofficial PubChem MCP Server?
Unofficial PubChem MCP Server works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.
Is Unofficial PubChem MCP Server free to use?
Yes, Unofficial PubChem MCP Server is open source and available under the NOASSERTION license. You can use it freely in both personal and commercial projects.
Unofficial PubChem MCP Server Alternatives — Similar Data Science & ML Servers
Looking for alternatives to Unofficial PubChem MCP Server? Here are other popular data science & ml servers you can use with Claude, Cursor, and VS Code.
Ultrarag
★ 5.6kA Low-Code MCP Framework for Building Complex and Innovative RAG Pipelines
RocketRide
★ 3.1k📇 🏠 - MCP server that exposes RocketRide AI pipelines as t
Aix Db
★ 2.1kAix-DB 基于 LangChain/LangGraph 框架，结合 MCP Skills 多智能体协作架构，实现自然语言到数据洞察的端到端转换。
NeMo Data Designer
★ 1.9k🎨 NeMo Data Designer: Generate high-quality synthetic data from scratch or from seed data.
PaperBanana
★ 1.7kOpen source implementation and extension of Google Research’s PaperBanana for automated academic figures, diagrams, and research visuals, expanded to new domains like slide generation.
MiniMax
★ 1.5kBridges MiniMax AI capabilities to the Model Context Protocol, enabling AI agents to perform image understanding, text-to-image generation, and speech synthesis. It provides a standardized interface for accessing MiniMax's core tools via JSON-RPC.
Browse More Data Science & ML MCP Servers
Explore all data science & ml servers available in the MCPgee directory. Each server includes setup guides for Claude, Cursor, and VS Code.
Set Up Unofficial PubChem MCP Server in Your Editor
Choose your AI client for step-by-step setup instructions.
Quick Config Preview
Add this to your claude_desktop_config.json or .cursor/mcp.json
Ready to use Unofficial PubChem MCP Server?
Browse our complete directory of 33,000+ MCP servers, read setup guides for your editor, and start building with the Model Context Protocol.