KEGG Connector for AI agents.
7 live capabilities
Query metabolic pathways and genomic data for bioinformatics research.
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Why people use KEGG
KEGG for Bioinformatics and Systems Biology Research
This Connector changes that by letting you ask your AI agent to do the heavy lifting. You just describe the biological system you're interested in, and the agent pulls the pathways, gene links, and chemical data into your chat.
What Vinkius changes
You get instant access to the world's most trusted biological database through simple chat commands.
Use it from Claude, ChatGPT, Cursor or another AI client you already have.
One account · 5,900+ Connectors
- Real-world use case 01
Drug Interaction Check
A pharmacologist asks the agent to check for interactions between two specific drugs to see if they're safe to use together.
- Real-world use case 02
Pathway Mapping
A researcher wants to see which metabolic pathways are affected by a specific human gene and gets a list of links.
- Real-world use case 03
Compound Search
A chemist needs the chemical data for a specific compound and asks the agent to find it by its molecular weight.
Complete set · 7capabilities
The complete KEGG capability set.
These are the exact actions your AI can choose when you ask it to work with KEGG.
01—04
4 capabilities in this set.
Part of 7 available through KEGG.
- 01 Capability
Kegg list
Kegg_list gets a list of entry identifiers and names. It lets you see all available organisms or pathways.
- 02 Capability
Kegg info
Kegg_info displays database release information and statistics. It helps you see the current state of the KEGG data.
- 03 Capability
Kegg link
Kegg_link finds related entries using database cross-references. Use it to see how genes map to pathways.
- 04 Capability
Kegg conv
Kegg_conv converts KEGG identifiers to and from outside databases. This saves time when moving between NCBI and PubChem.
05—07
3 capabilities in this set.
Part of 7 available through KEGG.
- 05 Capability
Kegg ddi
Kegg_ddi finds adverse drug-drug interactions. It is essential for clinical and pharmacological research.
- 06 Capability
Kegg find
Kegg_find finds entries matching a keyword or chemical data. You can search for compounds by mass or formula.
- 07 Capability
Kegg get
Kegg_get retrieves database entries in flat-file or specific file formats. It lets you grab the raw data for a specific entry.
Set up in minutes
One URL. Then ask KEGG to work.
Claude and ChatGPT only need the Connector URL. Copy it once, add it in settings, and use KEGG from the conversation.
Choose your client
Live previewAdvanced clients IDE · CLI
Claude · Web + desktop
Connector URL · ready to paste
Streamable HTTPhttps://edge.vinkius.com/vk_preview_3VQS6ta0LfpPfSufEA9QzNKVt9adBMSWJpS3FFGz/mcp - Step 01
Open Connectors
In Claude Web or Claude Desktop, open Settings and choose Connectors.
- Step 02
Add the URL
Choose Add custom connector, name it KEGG, and paste the URL above.
- Step 03
Turn it on in chat
Select +, open Connectors, and enable KEGG for the conversation.
ChatGPT · Web + desktop
Connector URL · ready to paste
Streamable HTTPhttps://edge.vinkius.com/vk_preview_3VQS6ta0LfpPfSufEA9QzNKVt9adBMSWJpS3FFGz/mcp - Step 01
Open MCP settings
On desktop, open Settings and MCP servers. On web, open your workspace app or connector settings.
- Step 02
Add the URL
Choose Add server with Streamable HTTP, or create a custom MCP app, then paste the KEGG URL.
- Step 03
Save and start
Save the connection and enable KEGG in your conversation. Desktop may ask you to restart once.
Cursor · IDE configuration
Advanced setup
{
"mcpServers": {
"kegg": {
"url": "https://edge.vinkius.com/vk_preview_3VQS6ta0LfpPfSufEA9QzNKVt9adBMSWJpS3FFGz/mcp"
}
}
}- Step 01
Open MCP Settings
Press Cmd+Shift+P (macOS) or Ctrl+Shift+P (Windows/Linux) → search "MCP Settings"
- Step 02
Add the server config
Paste the JSON configuration above into the mcp.json file that opens
- Step 03
Save the file
Cursor will automatically detect the new Connector
- Step 04
Start using KEGG
Open Agent mode in chat and ask: "Using KEGG, help me...". 7 tools available
VS Code Copilot · IDE configuration
Advanced setup
{
"mcpServers": {
"kegg": {
"url": "https://edge.vinkius.com/vk_preview_3VQS6ta0LfpPfSufEA9QzNKVt9adBMSWJpS3FFGz/mcp"
}
}
}- Step 01
Create MCP config
Create a .vscode/mcp.json file in your project root
- Step 02
Add the server config
Paste the JSON configuration above
- Step 03
Enable Agent mode
Open GitHub Copilot Chat and switch to Agent mode using the dropdown
- Step 04
Start using KEGG
Ask Copilot: "Using KEGG, help me...". 7 tools available
Windsurf · IDE configuration
Advanced setup
{
"mcpServers": {
"kegg": {
"url": "https://edge.vinkius.com/vk_preview_3VQS6ta0LfpPfSufEA9QzNKVt9adBMSWJpS3FFGz/mcp"
}
}
}- Step 01
Open MCP Settings
Go to Settings → MCP Configuration or press Cmd+Shift+P and search "MCP"
- Step 02
Add the server
Paste the JSON configuration above into mcp_config.json
- Step 03
Save and reload
Windsurf will detect the new server automatically
- Step 04
Start using KEGG
Open Cascade and ask: "Using KEGG, help me...". 7 tools available
Cline · IDE configuration
Advanced setup
{
"mcpServers": {
"kegg": {
"url": "https://edge.vinkius.com/vk_preview_3VQS6ta0LfpPfSufEA9QzNKVt9adBMSWJpS3FFGz/mcp"
}
}
}- Step 01
Open Cline MCP Settings
Click the Connectors icon in the Cline sidebar panel
- Step 02
Add remote server
Click "Add Connector" and paste the configuration above
- Step 03
Enable the server
Toggle the server switch to ON
- Step 04
Start using KEGG
Ask Cline: "Using KEGG, help me...". 7 tools available
Claude Code · Terminal command
Advanced setup
claude mcp add kegg --transport http "https://edge.vinkius.com/vk_preview_3VQS6ta0LfpPfSufEA9QzNKVt9adBMSWJpS3FFGz/mcp"- Step 01
Install Claude Code
Run npm install -g @anthropic-ai/claude-code if not already installed
- Step 02
Add the Connector
Run the command above in your terminal
- Step 03
Verify the connection
Run claude mcp to list connected servers, or type /mcp inside a session
- Step 04
Start using KEGG
Ask Claude: "Using KEGG, show me...". 7 tools are ready
Where the request belongs
Work KEGG can move forward.
Bioinformatics researchers and pharmacologists who are tired of manually scraping biological data or jumping between multiple database tabs to find cross-references.
Bioinformatics Researcher
Pulls gene sequences and pathway maps into analysis pipelines without manual REST calls.
Pharmacologist
Checks drug-drug interactions and chemical properties during drug discovery.
Data Scientist
Integrates biological metadata into research workflows using natural language queries.
Build the capability set
Add more capabilities.
Each Connector adds new actions and data without changing how you work.
Browse ConnectorsEnsembl
Access genomic data, gene trees, homologies, and cross-references from the Ensembl database directly from any AI agent.
GenBank/NCBI API
Access genomic data. audit sequences, proteins, and UIDs via IA.
UniProt
Search 250M+ protein sequences with functional annotations, gene names, subcellular locations, and amino acid data from the world's most comprehensive protein knowledge base.
PubChem PUG REST API
Access chemical data. audit compounds, formulas, and CIDs via AI.
EBI Proteins API
Query the UniProt knowledge base for protein sequences, annotations, and functional data across millions of characterized entries.
EBI InterPro
Classify protein sequences into families, predict functional domains, and explore evolutionary relationships across species.
Bring your own AI
Change the model, client or framework. Keep KEGG connected.
-
Claude -
ChatGPT -
Gemini -
Cursor -
VS Code -
Windsurf -
ZCode -
Cline -
Zed -
Continue -
Kiro -
Roo Code -
Zencoder -
Goose -
Void -
Augment Code -
Amp -
Qodo -
Tabnine -
Pieces -
Sourcegraph Cody -
JetBrains -
Warp -
Amazon Q -
Antigravity -
BoltAI -
Raycast -
Jan -
LM Studio -
AnythingLLM -
Open WebUI -
Msty -
Cherry Studio -
LibreChat -
TypingMind -
Chorus -
5ire -
n8n -
LangChain -
LlamaIndex -
CrewAI -
Vercel AI SDK
Before you connect
Questions about KEGG.
The practical details behind the request, access and result.
What is the KEGG MCP?
The KEGG MCP connects your AI agent to the Kyoto Encyclopedia of Genes and Genomes. It lets you query biological pathways, genomic data, and chemical information using natural language.
Can I use KEGG to find drug interactions?
Yes, you can use the KEGG MCP to identify adverse drug-drug interactions for pharmacological and clinical research.
Does it work with NCBI or PubChem IDs?
Yes, the Connector can convert identifiers between KEGG and other major databases like NCBI, UniProt, and PubChem.
Can I get raw data for a specific gene?
You can retrieve specific database entries in various formats, including flat-files, by asking your agent to pull the data for a specific ID.
Is this suitable for bioinformatics research?
It is a standard capability for bioinformatics. It helps researchers automate the retrieval of gene sequences and pathway maps.
How does the KEGG MCP help with drug discovery?
It allows pharmacologists to quickly check chemical properties and potential interactions between drugs during the discovery process.
How can I find all metabolic pathways associated with a specific human gene?
You can use the kegg_link capability. 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 capability 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 capability and provide the drug identifiers separated by a '+' sign (e.g., 'D00564+D00017') to find known adverse interactions.
One connection away
Give your agent a direct line to KEGG.
Connect KEGG once. Keep it beside 5,900+ managed Connectors when the next task needs more.
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