How to Use the EBI InterPro MCP in Mastra AI

Build reliable protein analysis pipelines in Mastra AI with automated retries and clear state management for every biological query.

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Connect EBI InterPro MCP to Mastra AI

Create your Vinkius account to connect EBI InterPro to Mastra AI 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 InterPro with Mastra AI

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Automated domain discovery in Mastra AI

Automate your classification workflows by linking `search_proteins` and `get_protein_entries` into a multi-step agent sequence. Mastra AI handles the execution flow, ensuring your agent finds all domain annotations for a given sequence. If a query to the EBI InterPro MCP Server hits a network hiccup, the framework manages the retry logic for you. You define the workflow, and the system ensures the data is captured.

Structural validation in Mastra AI workflows

Create a conditional branch that verifies a sequence against `get_entry_structures` before proceeding to taxonomic analysis. This keeps your pipeline clean and ensures you only proceed with valid structural matches. Your agents can decide which path to take based on the tool results. If `get_structure` returns null, your agent can branch to a different classification strategy immediately.

Taxonomic audit trails in Mastra AI

Log every taxonomic discovery using `get_entry_taxonomy` to maintain a record of your protein evolution research. You can deploy this agent setup to your cloud environment with one command. This approach gives you a reproducible audit trail for your biological research. Every tool call is tracked and managed, ensuring your Mastra AI agents stay on task.

Setup guide

Set up EBI InterPro MCP in Mastra AI

Prerequisites

Node.js 18+ and a TypeScript project
@mastra/mcp + @mastra/core packages
Active Vinkius subscription with a valid endpoint token

1

Install dependencies
Run npm install @mastra/mcp @mastra/core plus your preferred model provider (e.g. @ai-sdk/openai).
2

Configure the MCPClient
Create an MCPClient with your Vinkius endpoint as a URL object. Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com.
3

Discover and inject tools
Call mcpClient.listTools() and spread the result into your agent's tools object. All EBI InterPro tools become native Mastra tools.
4

Run with any model
Swap openai("gpt-4o") for any AI SDK-compatible provider. Call agent.generate() and the agent routes tool calls through MCP automatically.

agent.ts

import { MCPClient } from "@mastra/mcp";
import { Agent } from "@mastra/core/agent";
import { openai } from "@ai-sdk/openai";

const mcpClient = new MCPClient({
  id: "ebi-interpro-mcp-client",
  servers: {
    "ebi-interpro-mcp": {
      url: new URL(
        "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
      ),
    },
  },
});

const agent = new Agent({
  name: "EBI InterPro Agent",
  model: openai("gpt-4o"),
  instructions: "You have access to EBI InterPro tools.",
  tools: {
    ...(await mcpClient.listTools()),
  },
});

const result = await agent.generate(
  "List recent EBI InterPro transactions"
);
console.log(result.text);

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Common questions about EBI InterPro MCP in Mastra AI

They can. You define the agent tools, and the framework orchestrates the sequence of calls to the EBI InterPro server to perform multi-step analysis.

Configure your agent to use the framework's built-in retry and error handling. If a tool call fails, the agent will attempt to resolve it based on your defined policy.

All traffic between your agent and the server is encrypted via the Vinkius transport layer. We isolate your session to ensure your protein sequences remain private.

Yes, you can store previous tool results in the agent's memory. This allows your Mastra AI setup to reference previous findings while querying new proteins.

Use the tool approval feature in your agent definition. This forces the agent to pause before calling any sensitive tools, letting you verify the action manually.

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