BioMCP
A Model Context Protocol server that enhances language models with protein structure analysis capabilities, enabling detailed active site analysis and disease-related protein searches through established protein databases.
What is BioMCP?
BioMCP is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to model context protocol server that enhances language models with protein structure analysis capabilities, enabling detailed active site analysis and disease-related protein searches through establishe...
A Model Context Protocol server that enhances language models with protein structure analysis capabilities, enabling detailed active site analysis and disease-related protein searches through established protein databases.
This server falls under the Data Science & ML category on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- A Model Context Protocol server that enhances language model
Use Cases
Maintainer
Works with
Installation
NPM
npx -y biomcpManual Installation
npx -y biomcpConfiguration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use BioMCP
BioMCP is a unified biomedical research MCP server that gives language models a single command grammar to query multiple authoritative data sources including PubMed, ClinicalTrials.gov, ClinVar, gnomAD, UniProt, AlphaFold, ChEMBL, OpenFDA, GWAS Catalog, and more than a dozen others. With one query you can search literature, pivot to related genes, variants, drugs, diseases, proteins, pathways, and clinical trials without rebuilding your workflow for each API. Researchers, clinicians, and bioinformatics agents use BioMCP to accelerate evidence synthesis, identify drug-gene interactions, and explore disease mechanisms.
Prerequisites
- The biomcp binary installed via curl installer, uv tool install, or pip install biomcp-cli
- Python 3.11+ if installing via pip (the Rust binary works standalone without Python)
- Optional: Semantic Scholar API key set as S2_API_KEY environment variable for enhanced literature search
- Internet access to reach public biomedical APIs (PubMed, ClinicalTrials.gov, UniProt, etc.)
- An MCP client such as Claude Desktop
Install the BioMCP binary
The fastest installation is via the curl installer which downloads the correct pre-built binary for your platform. Alternatively use uv tool install or pip.
# Recommended: curl installer
curl -fsSL https://biomcp.org/install.sh | bash
# Or via uv
uv tool install biomcp-cli
# Or via pip
pip install biomcp-cliVerify installation and check APIs
Run a health check to confirm BioMCP is installed and can reach the upstream biomedical APIs.
biomcp health --apis-onlyTry your first query
Test BioMCP with a quick biomedical question. The 'suggest' command routes your question to worked examples and starter commands.
biomcp suggest "What drugs treat melanoma?"
biomcp get gene BRAF pathways hpa
biomcp search article -g BRAF --limit 5Install guided skills into your agent directory
Install BioMCP's built-in investigation workflow skills into your Claude config directory for richer agent-assisted research.
biomcp skill install ~/.claude --forceAdd BioMCP to your MCP client configuration
Add the BioMCP server to claude_desktop_config.json. The server is invoked with the 'serve' subcommand.
{
"mcpServers": {
"biomcp": {
"command": "biomcp",
"args": ["serve"]
}
}
}BioMCP Examples
Client configuration
Minimal claude_desktop_config.json for BioMCP. Add S2_API_KEY to env for enhanced Semantic Scholar article search.
{
"mcpServers": {
"biomcp": {
"command": "biomcp",
"args": ["serve"],
"env": {
"S2_API_KEY": "your-semantic-scholar-api-key-optional"
}
}
}
}Prompts to try
Research queries Claude can answer by querying PubMed, ClinicalTrials.gov, UniProt, ClinVar, and other biomedical databases through BioMCP.
- "Search for recent articles about BRAF V600E mutations in melanoma treatment"
- "Find all recruiting clinical trials for pembrolizumab in lung cancer"
- "Get the protein structure and known interactions for BRCA1"
- "What are the pharmacogenomics recommendations for CYP2D6 variants?"
- "Show me adverse event reports for metformin from the FDA FAERS database"Troubleshooting BioMCP
biomcp command not found after installation
The curl installer places the binary in ~/.local/bin or /usr/local/bin. Make sure that directory is in your PATH. Run 'echo $PATH' and add 'export PATH=$HOME/.local/bin:$PATH' to your ~/.bashrc or ~/.zshrc if needed.
API health checks fail for specific upstream sources
Run 'biomcp health --apis-only' to see which upstream sources are reachable. Public APIs like ClinicalTrials.gov and PubMed occasionally have rate limits or downtime. BioMCP will still function with the remaining available sources.
Article search returns fewer results than expected or misses Semantic Scholar results
Semantic Scholar integration is optional and requires an S2_API_KEY environment variable. Register for a free API key at https://www.semanticscholar.org/product/api and add it to your MCP server env block in claude_desktop_config.json.
Frequently Asked Questions about BioMCP
What is BioMCP?
BioMCP is a Model Context Protocol (MCP) server that model context protocol server that enhances language models with protein structure analysis capabilities, enabling detailed active site analysis and disease-related protein searches through established protein databases. It connects AI assistants to external tools and data sources through a standardized interface.
How do I install BioMCP?
Install via npm with the command: npx -y biomcp. Then add the server configuration to your AI client's JSON config file (e.g., claude_desktop_config.json or .cursor/mcp.json).
Which AI clients work with BioMCP?
BioMCP works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.
Is BioMCP free to use?
Yes, BioMCP is open source and available under the MIT License license. You can use it freely in both personal and commercial projects.
BioMCP Alternatives — Similar Data Science & ML Servers
Looking for alternatives to BioMCP? 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 BioMCP 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 BioMCP?
Browse our complete directory of 33,000+ MCP servers, read setup guides for your editor, and start building with the Model Context Protocol.