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Anthropic's Model Context Protocol (MCP): A Complete Guide

Introduction

Anthropic's Model Context Protocol (MCP) enables Claude to interact with external tools and data sources. This guide will walk you through every step of setting it up and using it for research purpose.

Step-by-Step Implementation

Step 1: Setting Up Claude Desktop

Visit https://claude.ai/download
Click "Download" for your operating system
Install the application:

Windows: Run the .exe file and follow installation prompts
Mac: Open .dmg file and drag Claude to Applications folder

Step 2: Getting Brave Search API Key

Visit https://api.search.brave.com/app/
Create accountClick "Sign Up", if you do not have already an account.
Log in to your account
Click "Create API Key"
Name your key (e.g., "Claude MCP")
Copy the API key - you'll need it for the next step

Step 3: Setting Up Configuration

Find your Claude configuration folder:
1. Mac: Open Finder, press Cmd+Shift+G, type ~/Library/Application Support/Claude
Create configuration file:
1. Create new file named exactly: claude-desktop-config.json
2. Copy this exact configuration:

3. Replace placeholders:

Replace YOUR_API_KEY_HERE with your Brave API key
Replace PATH_TO_YOUR_RESEARCH_FOLDER with your desired path
Create a research folder structure
Make sure this matches your allowed_paths in the config

Step 4: Testing Your Setup

Open Claude Desktop
Sign in with your Anthropic account
Test Brave Search with prompts as follows:

"Search for the latest papers about Explainable Graph Neural Networks"
You should see Claude asking permission to use Brave Search
Click "Allow"

Test File System:

Create a test file called 'test.txt' in my research folder
Claude should ask for file system permission
Click "Allow"

Use cases

1. Literature Search:

Copy and paste this prompt: "Search for papers about GNN explainability published in 2024.

For each paper extract:

- Title

- Authors

- Key methods

- Results Save the summary in /Users/usamaejaz/Desktop/gnn_xai_summary.txt"

2. Create Analysis

Copy and paste this prompt:

"Read the papers from the summary and create:

1. A comparison table of methods

2. Key findings summary

3. Future research directions

Save in /Users/usamaejaz/Desktop/gnn_xai_analysis.md"

Best Practice

Always verify search results
Keep organized folder structure
Use descriptive file names
Regular backups of research data
Test new workflows with sample data

Next Steps

Explore custom MCP servers
Create automated research workflows
Integrate with other tools such as Visual Studio Code to run/test/debug code real-time environment

Resources

Claude Documentation: https://docs.anthropic.com/claude/

Brave Search API: https://api.search.brave.com/docs

MCP GitHub: https://github.com/modelcontextprotocol/servers/tree/main

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