Vinkius
KEGG

KEGG MCP for AI. Query Genomic and Systemic Biological Data.

Claude Claude
ChatGPT ChatGPT
Cursor Cursor
Gemini Gemini
Windsurf Windsurf
VS Code VS Code
JetBrains JetBrains
Vercel Vercel
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KEGG MCP on Cursor AI Code EditorKEGG MCP on Claude Desktop AppKEGG MCP on OpenAI Agents SDKKEGG MCP on Visual Studio CodeKEGG MCP on GitHub Copilot AI AgentKEGG MCP on Google Gemini AIKEGG MCP on Lovable AI DevelopmentKEGG MCP on Mistral AI AgentsKEGG MCP on Amazon AWS Bedrock

How this MCP server connects to your AI agent

KEGG connects your AI agent directly to the Kyoto Encyclopedia of Genes and Genomes (KEGG). Query complex biological data—including metabolic pathways, gene sequences, chemical compounds, and drug interactions—using natural language.

It provides the gold standard for bioinformatics exploration without manual database calls.

What AI agents can do with KEGG Automation

Kegg conv

Converts a gene or compound identifier between KEGG and external databases like NCBI.

Kegg ddi

Searches for known adverse drug-drug interactions using chemical names or IDs.

Kegg find

Queries the database to locate entries based on general keywords or specific chemical data points.

+ 4 more capabilities included
Map biological pathways

Find related entries and visualize how genes link up into larger metabolic or signaling networks.

Analyze drug interactions

Identify specific adverse reactions between drugs, which is critical for pharmacology research.

Retrieve gene details

Fetch detailed records on genes, proteins, and associated organisms from the KEGG database.

Search chemical data

Find entries for compounds, glycans, or drugs using keywords or specific formulas.

Standardize identifiers

Convert a gene ID from one database (like NCBI) into another required format for analysis.

Included with Plan

Waiting for input…

AI Agent

What AI agents can do with KEGG with 7 Tools

These seven tools let you analyze identifiers, find drug interactions, and retrieve deep biological records directly from the KEGG database using your AI agent.

Make your AI actually useful.

Add this MCP to Claude, Cursor, or Windsurf and your AI stops guessing. It gets real tools to look things up, take action, and handle the stuff you keep doing by hand.

Start using KEGG on Vinkius

Kegg Conv

Converts a gene or compound identifier between KEGG and external databases like NCBI.

Kegg Ddi

Searches for known adverse drug-drug interactions using chemical names or IDs.

Kegg Find

Queries the database to locate entries based on general keywords or specific...

Kegg Get

Retrieves full, detailed records for a specified gene or pathway in various file...

Kegg Info

Displays system-level statistics and release information for the KEGG database...

Kegg Link

Identifies related biological entries by mapping cross-references between different pathway types.

Kegg List

Generates a comprehensive list of available identifiers, such as all known organisms or pathways.

Security and governance baked right in.

Pick your AI client below to get set up. Just create a Vinkius account, subscribe, and you're instantly up and running. We handle the entire backend infrastructure, delivering out-of-the-box support for HTTPS Streamable, SSE, and OAuth2—zero messy routing required.

Claude AI

Claude AI

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 integration is available immediately — no restart needed.

Choose How to Get Started

Build a custom MCP for your own tools, or connect a ready-made integration from our catalog.

Build Your Own

Turn any API into an MCP. Import a spec, define Agent Skills, or deploy with MCPFusion.

  • Import from OpenAPI, Swagger, or YAML specs
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Start building

Make Your AI Do More

Start with KEGG, then connect any of our 5,100+ other servers whenever your AI needs more. One click, no limits.

  • Use this MCP plus 5,100+ others, all in one place
  • Add new capabilities to your AI anytime you want
  • Every connection is secured and compliant automatically
  • Track usage and costs across all your servers
  • Works with Claude, ChatGPT, Cursor, and more
  • New servers added to the catalog every week
KEGG MCP server cover

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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Built on the Model Context Protocol (MCP) for Claude, ChatGPT, Cursor, and more

The Model Context Protocol standardizes how applications expose capabilities to LLMs. Instead of operating in isolation, your AI gains direct access to external platforms, live data, and real-world actions through secure, standardized connections.

This connection provides 7 powerful capabilities that interface natively with Claude, ChatGPT, Cursor, and other compatible AI platforms. No middleware. No custom integration required.

Keeping track of all biological identifiers across multiple databases is a nightmare., Solved with Vinkius AI Gateway

Today, if you find an interesting gene ID in one paper—say, from NCBI—and your analysis requires it to be mapped into a metabolic pathway tool that uses KEGG IDs, you spend time manually cross-referencing. You copy the ID, paste it somewhere else, wait for the conversion tool to run, and then hope the resulting format is compatible with the next piece of software.

With this MCP, your agent handles the headache. Instead of manual conversions, you just tell your AI client what you're working on. The system automatically uses `kegg_conv` behind the scenes to standardize that ID immediately, giving you clean data ready for pathway analysis.

Get structured metabolic pathways with KEGG MCP

Before, tracing a gene's role in a larger system meant opening multiple tabs: one for the gene details (`kegg_get`), another to find related pathways (`kegg_link`), and maybe a third just to see what organisms are involved (`kegg_list`). It’s constant switching between different data views.

Now, you ask your agent about the pathway. The system uses `kegg_link` and aggregates all that necessary cross-referencing into one clean answer. You don't navigate; you just get the final map.

What your AI can actually do with this

Need to map out a signaling cascade or check how two drugs might clash? This MCP gives your AI agent direct access to KEGG, one of the most important biological databases available. Instead of writing complex REST API calls and dealing with multiple data endpoints, you just ask your client a question about genes, pathways, or chemistry.

For example, if you're investigating novel drug targets, you can use the system to check for adverse drug-drug interactions before running any wet lab work. It handles everything from identifying basic gene identifiers to converting them across major databases like UniProt and NCBI. When your workflow hits a biological data wall—say, you need metabolic pathway details that aren't in standard literature—this MCP makes sure the information is right there for your agent to process.

Because Vinkius hosts this entire catalog of tools, connecting KEGG means all your core systems biology needs are covered from one place.

Built · Hosted · Managed by Vinkius KEGG MCP - Query Genomics & Pathway Data
Server ID 019e5d2a-8373-70db-b8ca-52af01909f7f
Vinkius Inspector
Compliance Grade A+
Score 100/100
Vinkius Inspector Badge — Score 100/100

Questions you might have

How do I find out what organisms are in KEGG using kegg_list? +

You run kegg_list and specify 'organism' as the parameter. This gives you a list of all available biological species tracked by the database, like Homo sapiens or Mus musculus.

Can I use kegg_ddi to check drug interactions for something not in KEGG? +

No; kegg_ddi requires compounds that are already cataloged within the KEGG system. If your compound is novel, you'll need to search for its chemical data first using kegg_find.

What do I use kegg_conv for? +

kegg_conv handles identifier translation. You pass it an ID from one system, and it reliably spits out the corresponding ID used by KEGG or other required external databases.

Does kegg_get give me all possible data formats? +

Yes. kegg_get retrieves detailed records for a gene or pathway, and it is designed to output the information in various structured file types that your agent can easily ingest.

How do I check the database status or release version using kegg_info? +

The kegg_info tool displays system metadata, including the current database release date and statistics. This confirms if you're working with the most recent dataset available for analysis.

What is the purpose of using kegg_link to find related entries? +

kegg_link finds associated data points using cross-references across different biological systems. You use it specifically when you need to map relationships, like linking a human gene to its relevant metabolic pathway.

Can I use kegg_find for chemical structures or just general keywords? +

kegg_find is flexible; it accepts multiple inputs. You can search using general keywords, specific formulas, or even molecular masses to pinpoint matching entries across various compound databases.

Does kegg_get provide raw data formats for genes and proteins? +

Yes, kegg_get retrieves comprehensive database entries in structured or flat-file formats. This allows you to pull detailed gene sequences or full protein information directly into your analysis pipeline.

How can I find all metabolic pathways associated with a specific human gene? +

You can use the kegg_link tool. Specify 'pathway' as the target_db and the human gene ID (e.g., 'hsa:10458') as the source_db to retrieve all linked biological pathways.

Can I search for chemical compounds using an exact molecular mass? +

Yes! Use the kegg_find tool with the database set to 'compound', the mass value as the query, and the option set to 'exact_mass'.

Is it possible to check for interactions between multiple drugs at once? +

Absolutely. Use the kegg_ddi tool and provide the drug identifiers separated by a '+' sign (e.g., 'D00564+D00017') to find known adverse interactions.

Built & Managed by Vinkius 30s setup 7 tools

We've already built the connector for KEGG. Just plug in your AI agents and start using Vinkius.

No hosting. No infrastructure. No complex setup.
All 7 tools are live and waiting. You're up and running in seconds.

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