BioMCP

by acashmoney

8 stars

Not rated

GitHub

About

Enhances large language models with protein structure analysis capabilities, including active site analysis and disease-protein searches, by connecting to the RCSB Protein Data Bank.

Details

Author: acashmoney
Repository: acashmoney/bio-mcp
GitHub stars: 8
Categories: Developer Tools, AI, Design, Search, Infrastructure, Database

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below
Plugin Name BioMCP

Command (node, npx, python, etc.) node
Arguments
- Argument 1 /path/to/your/build/index.js
Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

JSON

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

From the repository

To install BioMCP for Claude Desktop automatically via Smithery:

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

npm install

1. Start the BioMCP server:

bash
npm start



2. In a separate terminal, install the MCP Inspector globally (if not already installed):

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



3. Launch the MCP Inspector and connect to your local BioMCP server:

bash
npx @modelcontextprotocol/inspector node build/index.js

4. Use the inspector interface to test tools and view responses. When integrated with a compatible language model, Bio-MCP enables queries like: - "What are the key residues in the active site of PDB structure 6LU7?" - "Find proteins related to Alzheimer's disease"

Run all tests:

bash
npm test



Run specific test suites:

bash

`analyze-active-site`

Provides detailed information about protein binding sites using a PDB ID.

`search-disease-proteins`

Returns proteins related to specified diseases or medical conditions.

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

{
    "mcpServers": {
        "biomcp": {
            "cwd": "",
            "env": {},
            "args": [
                "/path/to/your/build/index.js"
            ],
            "shell": false,
            "command": "node"
        }
    }
}

Linux

{
    "cwd": "",
    "env": [],
    "args": [
        "/path/to/your/build/index.js"
    ],
    "shell": false,
    "command": "node"
}

Macos

{
    "cwd": "",
    "env": [],
    "args": [
        "/path/to/your/build/index.js"
    ],
    "shell": false,
    "command": "node"
}

Windows

{
    "cwd": "",
    "env": [],
    "args": [
        "/path/to/your/build/index.js"
    ],
    "shell": false,
    "command": "node"
}

BioMCP: Enabling agent-based biomedical R&D

BioMCP

Overview

BioMCP is a Model Context Protocol (MCP) server designed to enhance large language models with protein structure analysis capabilities. It provides tools for analyzing protein active sites and searching for disease-related proteins by interfacing with established protein databases.

Future work will be centered around enabling agents to utilize the BioMCP.

Features

Technical Details

BioMCP implements the Model Context Protocol, allowing language models to access specialized protein structure knowledge without requiring this information to be part of their training data. The server handles API connections, data formatting, and error handling to provide reliable protein structure insights.

API Endpoints

BioMCP exposes two primary tools:

1. analyze-active-site: Provides detailed information about protein binding sites using a PDB ID
2. search-disease-proteins: Returns proteins related to specified diseases or medical conditions

Getting Started

Installing via Smithery

To install BioMCP for Claude Desktop automatically via Smithery:

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

Manual Installation

```bash

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Details

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Setting up with Highlight

From the repository

analyze-active-site

search-disease-proteins

Claude Desktop / Cursor

Linux

Macos

Windows

BioMCP: Enabling agent-based biomedical R&D

Overview

Features

Technical Details

API Endpoints

Getting Started

Installing via Smithery

Manual Installation

Install

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Context 7

1Panel

`analyze-active-site`

`search-disease-proteins`