How to Use the UniProt MCP in Windsurf

Q: How can UniProt help me search by gene using Windsurf?

You run searchuniprotgene and it immediately returns all isoforms linked to that specific gene. Cascade figures out which protein variants are available, giving you a full picture of the protein family.

Q: Can UniProt help me get details for an accession ID with Windsurf?

Yep. Just feed getuniprotprotein the accesssion ID and it pulls all available data points, including subcellular location and sequence information. It's a straightforward call that gives you maximum context.

Q: If I need to find a specific type of hemoglobin using UniProt with Windsurf, how do I start?

You use the searchuniprot tool and input 'hemoglobin' as your keyword. The search returns protein names, gene origins, and functional descriptions that match that term in the UniProt database.

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Connect UniProt MCP to Windsurf

Create your Vinkius account to connect UniProt to Windsurf 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 UniProt with Windsurf

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Find full details on a specific protein.

Need all the data for one UniProt accession ID? Use `get_uniprot_protein` to pull every detail you need, like amino acid composition and functional notes. It gives you a complete profile instantly.

Search large databases by keyword or function.

Don't know the ID but know what it does? `search_uniprot` lets you search across the whole UniProt database using names, functions, or keywords. You can try looking up things like 'insulin' or 'p53'.

Map proteins back to their originating gene.

When you have a gene name but need protein details, `search_uniprot_gene` is your go-to. It returns all known isoforms and what they do. This helps narrow down exactly which protein variant you're looking at.

Setup guide

Set up UniProt MCP in Windsurf

Prerequisites

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

1

Open MCP configuration

Click the Cascade assistant icon in the sidebar, then click the hammer icon (🔨) at the top of the panel. Select "Configure" to open ~/.codeium/windsurf/mcp_config.json.
2

Add the UniProt MCP

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

Refresh MCPs

Go back to the hammer icon (🔨) in Cascade and click "Refresh". Windsurf will detect the new server. No full restart is needed — the connection is hot-reloaded.
4

Verify in Cascade

Start a new Cascade conversation and ask something like "Show my UniProt payment history." If connected, Cascade will call the UniProt tools directly. You will see a green dot next to the server name in the MCP panel.

mcp_config.json

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

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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.

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Common questions about UniProt MCP in Windsurf

You run `search_uniprot_gene` and it immediately returns all isoforms linked to that specific gene. Cascade figures out which protein variants are available, giving you a full picture of the protein family.

Yep. Just feed `get_uniprot_protein` the accesssion ID and it pulls all available data points, including subcellular location and sequence information. It's a straightforward call that gives you maximum context.

UniProt supports searching by name, function, or keyword using the `search_uniprot` tool. You don't need an ID; you just tell it what you're interested in and it handles the massive database lookup for you.

This server only touches publicly available protein sequences, functional annotations, and gene names. It doesn't handle any user-specific or protected health information.

You use the `search_uniprot` tool and input 'hemoglobin' as your keyword. The search returns protein names, gene origins, and functional descriptions that match that term in the UniProt database.

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