How to Use the EBI Proteins API MCP in Windsurf

Bring UniProt data directly into your Windsurf workspace. Cascade chains protein queries to build functional bioinformatics context.

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Connect EBI Proteins API MCP to Windsurf

Create your Vinkius account to connect EBI Proteins API 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 EBI Proteins API with Windsurf

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Claude

Perplexity

Autonomous Protein Data Retrieval

Stop manual lookups. Cascade uses `get_protein` and `get_protein_features` to pull sequence annotations directly into your editor. You define the accession, and your agent fetches the domain, signal peptide, and binding site data. This MCP Server provides the raw context your agent needs to understand structural features. It eliminates the need for external browser tabs while you work on protein-related code.

Variant Analysis for Windsurf

Analyze clinical significance without leaving your IDE. Cascade uses `get_variation` to map specific mutations to their functional consequences. It cross-references wild-type and mutant residues to show you exactly how a variant impacts protein stability. Your agent can chain these queries to investigate entire proteomes. It uses `search_variation` to filter by consequence type, giving you an immediate view of clinical relevance across your project.

Genomic Mapping and Taxonomy

Bridge the gap between protein and genome. Cascade uses `get_coordinates` to pull Ensembl data for any UniProt accession. It ensures your code stays synced with the correct chromosome and strand positions. Use `get_taxonomy` or `search_taxonomy` to resolve organism identifiers within the same context. Your agent handles the lineage lookups, so you focus on the logic.

Setup guide

Set up EBI Proteins API 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 EBI Proteins API 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 EBI Proteins API payment history." If connected, Cascade will call the EBI Proteins API tools directly. You will see a green dot next to the server name in the MCP panel.

mcp_config.json

{
  "mcpServers": {
    "ebi-proteins-api-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 EMBL-EBI Proteins API. 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 EBI Proteins API MCP in Windsurf

Open your Cascade prompt and ask it to find protein data by gene name or keyword. It will use the `search_proteins` tool to return a list of matches, allowing you to select the correct entry for further investigation.

Yes. You can instruct your agent to iterate over a list of accessions using the available tools. It will pull specific data points for each protein sequentially to complete your task.

Absolutely. Use the taxonomy tools to identify the correct organism IDs, then query the corresponding proteome data. The agent handles the mapping between different taxonomic ranks and their associated protein sets.

Vinkius handles authentication through a single endpoint token. You don't need to manage API keys locally; the server provides secure, authorized access directly to your agent.

This server only performs read operations against public UniProt endpoints. No proprietary sequence data or user-specific code leaves your machine, as the MCP protocol restricts communication to the defined tool outputs.

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