How to Use the EBI Proteins API MCP in Claude Code

Claude Code connects to the EBI Proteins API for headless bioinformatics pipelines. Automate protein lookups directly from your terminal.

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Connect EBI Proteins API MCP to Claude Code

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

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Headless Protein Lookups

Integrate `get_protein` directly into your shell scripts. Claude Code fetches UniProt entries as JSON, making it easy to pipe output into downstream analysis tools or logging services. This is designed for CI/CD environments where terminal access is the only interface. You get programmatic access to protein sequences without any browser overhead.

Taxonomy Resolution via CLI

Resolve taxon IDs in your automation pipelines using `search_taxonomy`. Claude Code finds the correct organism ID based on your input string, ensuring your subsequent queries target the right species. This prevents errors in automated workflows. The agent verifies the organism metadata before the pipeline proceeds to fetch proteome or variant data.

Variant Analysis for Pipelines

Run `search_variation` as part of your nightly builds. Claude Code tracks consequence types across protein sets, alerting you to new clinical annotations in your datasets. You maintain version control over your variant lookups. The agent logs the API output, which you can then compare against previous runs to detect changes in clinical status.

Setup guide

Set up EBI Proteins API MCP in Claude Code

Prerequisites

Claude Code CLI installed (npm install -g @anthropic-ai/claude-code)
Active Vinkius subscription with a valid endpoint token

1

Run the add command

Open your terminal and run the command shown on the right. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com. Use --scope user to make it available across all projects.
2

Verify the connection

Start a Claude Code session and type /mcp to list connected servers. You should see ebi-proteins-api-mcp with a green status indicator.
3

Start using tools

Ask Claude Code something like "Check my latest EBI Proteins API transactions." It will automatically discover and invoke the available EBI Proteins API tools.

Terminal

claude mcp add --transport http ebi-proteins-api-mcp https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

Get your connection token →

Prerequisites

Claude Code CLI installed
Active Vinkius subscription with a valid endpoint token

1

Open the config file

Create or edit .mcp.json in your project root for project-level scope, or ~/.claude.json for user-level scope.
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

Restart Claude Code

Start a new Claude Code session. Type /mcp to confirm the server is connected. The tools will be automatically available in your conversation.

.mcp.json

{
  "mcpServers": {
    "ebi-proteins-api-mcp": {
      "type": "url",
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

Get your connection token →

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Common questions about EBI Proteins API MCP in Claude Code

Use the CLI to prompt Claude Code with your specific protein query. It invokes the `search_proteins` tool and prints the result to your terminal, which you can then redirect to a file or pipe into another command.

Yes. You can write scripts that call the MCP tools via the Claude Code interface. It executes these commands in sequence, handling the data flow between tools for your automated tasks.

The server provides a direct interface to the EBI REST endpoints. As long as the public API is available, your Claude Code jobs will receive the expected JSON payloads for their processing steps.

You configure the server with a single Vinkius endpoint token in your `~/.claude.json` file. Authentication is handled at the transport layer, keeping your CLI commands clean and focused on your work.

Vinkius uses an ephemeral sandbox for these operations. The server does not log your specific queries or personal identifiers; it only processes the public protein data requested during your active session.

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