How to Use the KEGG MCP in Claude

Q: How do I install the KEGG MCP server in Claude Desktop?

Open your claudedesktopconfig.json file and add the server command under the mcpServers block. Restart the app completely to load the tools.

Q: Can Claude Desktop search KEGG by chemical structure?

Yes, you can use keggfind to search by chemical data. The agent will return the matching compound entries directly in your chat.

Q: Does this MCP setup handle bulk pathway downloads?

The kegglist tool pulls lists of identifiers, and keggget grabs the flat files. But if you need massive bulk downloads, you might hit API limits.

Q: How do I convert NCBI IDs to KEGG within Claude Desktop?

Just paste your NCBI IDs into the prompt. The agent calls keggconv to translate them automatically before running further queries.

Pull KEGG genomic data and drug interactions directly into Claude Desktop for your bioinformatics research.

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Connect KEGG MCP to Claude Desktop

Create your Vinkius account to connect KEGG to Claude Desktop and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

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Setup KEGG with Claude Desktop

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Map Pathways in Claude Desktop

The `kegg_get` tool retrieves complete biological pathways and flat-file genomic records right into your Claude Desktop chat. You don't have to leave the interface to grab specific human gene entries or compound structures. Just ask the agent to pull the exact identifier, and it prints the raw file data on your screen. If you only have partial chemical data, `kegg_find` steps in to locate the exact matches. Claude reads the results and summarizes the metabolic links immediately. You get the biochemical context without opening a browser tab.

Cross-Reference External IDs

The `kegg_conv` tool translates outside identifiers into native KEGG formats so your agent can actually read them. When you paste an NCBI Gene ID into the Claude web interface, this MCP Server maps it straight to the corresponding KEGG gene. It fixes the classic bioinformatics headache of mismatched naming conventions. Once the IDs line up, `kegg_link` finds related entries across different databases. Your agent can trace a specific gene to all associated human pathways in seconds. It connects the dots between raw sequence data and functional biology.

Check Drug Interactions Fast

The `kegg_ddi` tool flags adverse drug-drug interactions before you finalize your research notes. You hand Claude a list of chemical compounds, and it queries the database for known metabolic conflicts. The response hits your chat window instantly. Before running bulk queries, you can use `kegg_info` to check the current database release version. Then `kegg_list` grabs the full index of available organisms or pathways. You always know exactly what dataset your agent is working against.

Setup guide

Set up KEGG MCP in Claude Web or Desktop

1

Open Claude Settings

Go to claude.ai, click your profile icon, then navigate to Customize → Connectors.
2

Add Custom Connector

Click the "+" button and select Add custom connector. Paste your Vinkius endpoint URL: https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com. For OAuth-protected servers, expand Advanced settings to add credentials.
3

Start a conversation

Open a new chat. The KEGG MCP tools are available immediately — no restart needed.

Endpoint URL

https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

No configuration file needed — paste the URL directly in the Claude web interface.

Available on Free (1 connector), Pro, Max, Team, and Enterprise plans.

Prerequisites

Claude Desktop installed (macOS or Windows)
Active Vinkius subscription with a valid endpoint token

1

Open Claude Desktop Settings

Click the menu icon at the top-left corner, go to Settings → Developer → Edit Config. This opens claude_desktop_config.json in your default text editor.
2

Paste the KEGG MCP configuration

Copy the JSON snippet on the right into the mcpServers object. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Restart Claude Desktop

Close and reopen the application. Claude needs a full restart to load new MCPs — refreshing a conversation is not enough.
4

Verify the connection

Open a new conversation. Click the 🔌 icon at the bottom of the message input. You should see tools listed under kegg-mcp.

json

{
  "mcpServers": {
    "kegg-mcp": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

Get your connection token →

Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by KEGG. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about KEGG MCP in Claude Desktop

Open your `claude_desktop_config.json` file and add the server command under the `mcpServers` block. Restart the app completely to load the tools.

Yes, you can use `kegg_find` to search by chemical data. The agent will return the matching compound entries directly in your chat.

The `kegg_list` tool pulls lists of identifiers, and `kegg_get` grabs the flat files. But if you need massive bulk downloads, you might hit API limits.

Just paste your NCBI IDs into the prompt. The agent calls `kegg_conv` to translate them automatically before running further queries.

Claude routes your queries securely. The only data transmitted is the specific gene, pathway, or chemical identifier you ask to look up. Your broader research context stays local to your machine.

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