How to Use the EBI Proteins API MCP in Claude

Q: How do I configure the EBI Proteins API with Claude Desktop?

Open your claudedesktopconfig.json file and add the server configuration under the mcpServers key. Once you save the file and restart Claude Desktop, the MCP Server's 16 protein analysis tools will appear right in your chat window.

Q: Can Claude Desktop search for specific variants using the EBI Proteins API?

Yes, the client uses searchvariation to filter genetic variants by consequence type or source. It parses the results directly in your chat, saving you from downloading massive flatfiles.

Q: Does the EBI Proteins API on Claude Desktop support taxonomy lookups?

Absolutely. Your agent calls searchtaxonomy and gettaxonomy to resolve organism names and retrieve scientific lineages. You get accurate taxon IDs for your downstream protein queries without leaving the app.

Query UniProt sequences, mutagenesis data, and genetic variants directly inside Claude Desktop without leaving your chat window.

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Create your Vinkius account to connect EBI Proteins API to Claude Desktop 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 Claude Desktop

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Query UniProt entries inside Claude Desktop

Your agent queries protein sequences and molecular coordinates directly within your workspace using `get_protein` and `get_coordinates`. You get immediate access to UniProt accessions like P01308 without switching to a web browser or running external scripts. This MCP Server feeds raw sequence data directly into your chat window. It lets you analyze physical coordinates alongside genetic mappings to speed up your annotation tasks.

Analyze mutagenesis and variant annotations

Run `get_mutagenesis` and `get_variation` to pull phenotypic effects and clinical significance of amino acid changes. Your agent parses these complex datasets instantly, showing you wild-type and mutant residues side by side. Instead of manual parsing, you feed variant data directly into your local analysis. You get clear, structured outputs that connect genetic variants to functional protein disruptions.

Map proteomes and taxonomy nodes instantly

Use `get_proteome` and `get_taxonomy` to retrieve reference proteomes and scientific lineages directly in your workspace. You supply the NCBI taxon ID, and the tool outputs the parent and children nodes. This MCP integration speeds up comparative genomics by resolving taxonomic queries on the fly. You bypass manual database lookups and keep your focus on biological analysis.

Setup guide

Set up EBI Proteins API MCP in Claude Web or Desktop

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 EBI Proteins API MCP tools are available immediately — no restart needed.

Endpoint URL

https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

No configuration file needed — paste the URL directly in the Claude web interface.

Available on Free (1 connector), Pro, Max, Team, and Enterprise plans.

Prerequisites

Claude Desktop installed (macOS or Windows)
Active Vinkius subscription with a valid endpoint token

1

Open Claude Desktop Settings

Click the menu icon at the top-left corner, go to Settings → Developer → Edit Config. This opens claude_desktop_config.json in your default text editor.
2

Paste the EBI Proteins API MCP configuration

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

Restart Claude Desktop

Close and reopen the application. Claude needs a full restart to load new MCPs — refreshing a conversation is not enough.
4

Verify the connection

Open a new conversation. Click the 🔌 icon at the bottom of the message input. You should see tools listed under ebi-proteins-api-mcp.

json

{
  "mcpServers": {
    "ebi-proteins-api-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 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 Claude Desktop

Open your `claude_desktop_config.json` file and add the server configuration under the `mcpServers` key. Once you save the file and restart Claude Desktop, the MCP Server's 16 protein analysis tools will appear right in your chat window.

Yes, the client uses `search_variation` to filter genetic variants by consequence type or source. It parses the results directly in your chat, saving you from downloading massive flatfiles.

Absolutely. Your agent calls `search_taxonomy` and `get_taxonomy` to resolve organism names and retrieve scientific lineages. You get accurate taxon IDs for your downstream protein queries without leaving the app.

You can fetch active sites, binding domains, and transmembrane regions using `get_protein_features`. The tool returns exact sequence positions and experimental evidence counts directly to your agent.

Your queries for UniProt accessions and genetic variants run through a secure V8 isolate sandbox on Vinkius. This MCP setup ensures no local protein data or private sequence queries are stored or shared with third parties.

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