How to Use the KEGG MCP in Cursor

Q: How do I add the KEGG MCP server to Cursor?

Create a .cursor/mcp.json file in your project root. Add the server configuration there, and toggle Agent mode on in the chat panel.

Q: Will Cursor write types for KEGG drug interactions?

Yes. The agent calls keggddi, reads the exact response shape, and generates accurate TypeScript interfaces for your codebase.

Q: Can the AI find specific metabolic pathways?

It uses keggfind to search keywords and kegglist to pull the full index. The results drop right into your editor.

Q: How does Cursor handle external database IDs with KEGG?

The agent uses keggconv to translate identifiers on the fly. It can write the exact translation layer for your application using live data.

Write genomic analysis scripts in Cursor while the AI agent pulls live KEGG pathways and drug interactions into your code.

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Connect KEGG MCP to Cursor

Create your Vinkius account to connect KEGG to Cursor 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 Cursor

Ask AI about this MCP

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Claude

Perplexity

Live KEGG Data in Cursor

The `kegg_get` tool injects flat-file database entries straight into your active editor buffer. When you ask Cursor to write a Python script for pathway analysis, the agent fetches the actual human gene records to test the logic. You get working code that handles real biological formats, not empty string variables. The `kegg_info` tool confirms the exact database release you are hitting. This guarantees your data processing scripts match the current schema. You never write parsers for outdated file structures again.

Automate ID Conversion

The `kegg_conv` tool translates external bioinformatics IDs into KEGG identifiers while you write code. If your script ingests Uniprot IDs, Cursor calls this MCP Server to map them dynamically. Your agent writes the exact mapping functions you need based on live API responses. After conversion, `kegg_link` builds the cross-references. You can tell the IDE to generate a graph of related pathways, and it pulls the exact linked entries. The generated code actually runs because it uses real database relationships.

Code Drug Interaction Tools

The `kegg_ddi` tool checks for adverse drug-drug interactions right in your IDE. If you are building a clinical decision support app, Cursor can query this endpoint to structure your error-handling logic. It sees the real JSON response and types your TypeScript interfaces perfectly. For broader searches, `kegg_find` and `kegg_list` let the agent explore available organisms and chemical data. You just type a comment asking for a specific metabolic pathway list, and the editor fills in the exact array.

Setup guide

Set up KEGG MCP in Cursor

Prerequisites

Cursor installed (macOS, Windows, or Linux)
Active Vinkius subscription with a valid endpoint token

1

Open MCP Settings

Go to Cursor Settings → MCP or open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P) and search for "MCP: Add Server".
2

Add the KEGG MCP

Cursor will create or open .cursor/mcp.json in your project root. Paste the JSON snippet on the right. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Enable Agent mode

Open Composer (Cmd+I / Ctrl+I) and switch to Agent mode using the dropdown at the top. MCP tools are only available in Agent mode.
4

Verify the connection

Ask Cursor something like "List my recent KEGG transactions." If the MCP tools are loaded correctly, Cursor will call the KEGG tools automatically. You can also check Settings → MCP for a green status indicator.

.cursor/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 Cursor

Create a `.cursor/mcp.json` file in your project root. Add the server configuration there, and toggle Agent mode on in the chat panel.

Yes. The agent calls `kegg_ddi`, reads the exact response shape, and generates accurate TypeScript interfaces for your codebase.

It uses `kegg_find` to search keywords and `kegg_list` to pull the full index. The results drop right into your editor.

The agent uses `kegg_conv` to translate identifiers on the fly. It can write the exact translation layer for your application using live data.

Your local codebase remains entirely on your machine. The only information sent externally is the specific chemical structure or drug identifier you explicitly query against the API.

Use it with your favorite AI tools

Connect this server to Cursor, Claude, VS Code, and more.

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