Biomcp

🚀 BioMCP: Model Context Protocol Server for Enhanced Agent-Based Biomedical R&D

BioMCP is a server based on the Model Context Protocol (MCP), aiming to enhance the protein structure analysis capabilities of large language models. It offers functions to analyze protein active sites and search for disease-related proteins, and interfaces with existing protein databases.

🚀 Quick Start

Installation

Install via Smithery

To automatically install BioMCP for Claude Desktop via Smithery:

npx -y @smithery/cli install @acashmoney/bio-mcp --client claude

Manual Installation

# Clone the repository
git clone https://github.com/acashmoney/bio-mcp.git

# Install dependencies
npm install

# Start the server
npm start

Setup Instructions

Run the MCP Inspector

1. Start the BioMCP server:

   npm start
   

2. Globally install the MCP inspector in a separate terminal (if not already installed):

   npm install -g @anthropic-ai/mcp-inspector
   

3. Open the MCP inspector and connect to the local BioMCP server:

   npx @modelcontextprotocol/inspector node build/index.js
   

4. Use the inspector interface to test the tools and view responses.

Use with Claude Desktop

1. Build the BioMCP server:

   npm run build
   

2. Configure Claude Desktop to start the MCP server:

   a. Locate your Claude Desktop config.json file (usually in the user directory).

   b. Edit config.json to include the BioMCP server build path. Example configuration:

   {
     "globalShortcut": "",
     "mcpServers": {
       "bio-mcp": {
         "command": "node",
         "args": [
           "/path/to/your/build/index.js"
         ]
       }
     }
   }
   

3. Restart Claude Desktop after installation.

✨ Features

• Active Site Analysis: Check the binding sites and functional residues of proteins using PDB identifiers (PDB ID).
• Disease-Related Protein Search: Find protein structures associated with specific diseases or medical conditions.
• Integrated Data Access: Seamlessly connect to the RCSB Protein Data Bank (PDB)[https://www.rcsb.org/].

🔧 Technical Details

BioMCP implements the Model Context Protocol, enabling language models to access specialized protein structure knowledge without incorporating this information into their training data. The server handles API connections, data formatting, and error handling to provide reliable insights into protein structures.

📚 Documentation

API Endpoints

BioMCP mainly exposes two tools:

1. analyze-active-site: Provide detailed information on protein binding sites using a PDB ID.
2. search-disease-proteins: Return proteins associated with a specified disease or medical condition.

📄 Other Information

• Project repository: https://github.com/acashmoney/bio-mcp
• Documentation: https://github.com/acashmoney/bio-mcp/blob/main/README.md

🎯 Project Goals

• Introduce an agent-based biomedical research pipeline.
• Develop a client with protein visualization tools.