How to Use the UniProt MCP in Cline

Q: How do I map genes to proteins using UniProt with Cline?

Use searchuniprotgene. This function returns every protein isoform and its functional annotations for a given gene. You can then use that structured list in your code to build comprehensive data models.

Q: If I need details on one UniProt entry, how do I get it using Cline?

You call getuniprotprotein and supply the accession ID. The tool fetches all necessary protein details right into your terminal session, ready for testing or file generation.

Q: What keywords can UniProt search for with Cline?

You use searchuniprot to look up proteins by name, function, or any keyword. This lets you query the entire database without needing a specific ID first. Try 'BRCA1' or 'p53'.

Q: Can I find a specific gene's proteins using UniProt with Cline?

Absolutely. searchuniprotgene handles this by returning all associated protein isoforms and their annotations when you pass the gene name to it. This makes complex data retrieval easy.

Execute biological data workflows with Cline on the UniProt MCP Server.

See Vinkius in Action

Works with every AI agent you already use

…and any MCP-compatible client

MCP Servers - Free for Subscribers

Connect UniProt MCP to Cline

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

GDPR Free for Subscribers

Setup UniProt with Cline

Ask AI about this MCP

ChatGPT

Claude

Perplexity

Fetch complete protein profiles for immediate code use.

When you need a full UniProt profile, run `get_uniprot_protein`. This tool grabs all associated data—like the sequence and location—and outputs it directly into your working environment. You can then pipe that data straight into component creation.

Run targeted searches against UniProt annotations.

Start with `search_uniprot` to find proteins using general keywords like 'spike protein'. Cline handles the API call, retrieves the list of matching proteins, and lets you stage that resulting data for commits. It's ideal for build tasks.

Map genes to all their known UniProt isoforms.

To find every possible protein variant from a single gene, use `search_uniprot_gene`. This tool returns all functional annotations and isoforms. You can then write code that processes this list of variants automatically.

Setup guide

Set up UniProt MCP in Cline

Prerequisites

VS Code with Cline extension installed
Active Vinkius subscription with a valid endpoint token

1

Open Cline MCP settings

Click the Cline icon in the VS Code sidebar to open the Cline panel. Then click the MCP Servers icon (server stack) at the top-right corner of the panel.
2

Add a remote server

Click "Remote Servers" at the top, then click "Add Remote MCP". In the Name field, type uniprot-mcp. In the URL field, paste your Vinkius endpoint: https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp. Get your token from cloud.vinkius.com.
3

Enable the server

After saving, the server appears in the Cline MCP panel. Toggle the switch to enable it. The status indicator turns green when the connection is live.
4

Start using tools

Return to the Cline chat and ask: "Check my latest UniProt refund status." Cline will discover the available tools and request your approval before invoking each one — giving you full control over every action.

Cline MCP Settings

{
  "mcpServers": {
    "uniprot-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 UniProt. 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.

Why Choose Vinkius

Vinkius connects your tools to AI with real-time monitoring and automatic cost savings — all from one dashboard.

Connect UniProt now

Real-time monitoring

Live

visibility into every interaction

Connect your favorite tools to your AI and see exactly what's happening — every request, every response, in real time.

Built-in savings

60%

lower AI costs

Vinkius compresses data between your apps and your AI automatically. Lower bills every month — no configuration required.

Single dashboard

One

place for every integration

Every tool your AI connects to, managed from a single screen. One account, complete control.

Common questions about UniProt MCP in Cline

Use `search_uniprot_gene`. This function returns every protein isoform and its functional annotations for a given gene. You can then use that structured list in your code to build comprehensive data models.

You call `get_uniprot_protein` and supply the accession ID. The tool fetches all necessary protein details right into your terminal session, ready for testing or file generation.

You use `search_uniprot` to look up proteins by name, function, or any keyword. This lets you query the entire database without needing a specific ID first. Try 'BRCA1' or 'p53'.

The server only handles publicly sourced amino acid data, protein sequences, and functional annotations from the massive UniProt knowledge base. No private user data is involved.

Absolutely. `search_uniprot_gene` handles this by returning all associated protein isoforms and their annotations when you pass the gene name to it. This makes complex data retrieval easy.

Use it with your favorite AI tools

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

OpenAI Agents SDK sdk-python

Google ADK sdk-python

Pydantic AI sdk-python

Vercel AI SDK sdk-typescript