How to Use the EBI PDBe MCP in Mastra AI

Q: How do I map UniProt IDs to PDB entries using EBI PDBe in Mastra AI?

Use the getuniprotmapping tool. The agent takes the UniProt accession as input and returns the corresponding PDB chains for your workflow.

Build reliable bioinformatics workflows in Mastra AI with the EBI PDBe MCP Server for automated structural analysis.

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Connect EBI PDBe MCP to Mastra AI

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

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Claude

Perplexity

Automated quaternary structure analysis

Use `get_assemblies` to define the functional biological unit of a protein. Your Mastra workflow can branch based on whether the protein is a monomer or a complex. This automates the decision-making process for your agents. If a complex is detected, the agent triggers further analysis of the quaternary interfaces.

Validate protein quality in agent workflows

Run `get_quality_scores` as a prerequisite step in your pipeline. If the resolution or R-factor falls outside your thresholds, the agent skips that entry. This ensures your downstream modeling only uses reliable structures. You handle failures by having the agent flag the entry for manual review.

Extract binding sites for docking

Call `get_binding_sites` to identify key residues for molecular docking tasks. The agent extracts these coordinates to inform subsequent simulation steps. You build a complete chain from structure identification to site analysis. The workflow engine manages the retries if the network connection to the server flickers.

Setup guide

Set up EBI PDBe 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 PDBe 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-pdbe-mcp-client",
  servers: {
    "ebi-pdbe-mcp": {
      url: new URL(
        "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
      ),
    },
  },
});

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

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

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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 PDBe (Protein Data Bank in Europe). 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 PDBe MCP in Mastra AI

You initialize the server in your Mastra agent configuration using the provided endpoint. Once registered, you can add any of the 16 tools to your agent's capabilities.

Mastra handles retries natively. You can set up exponential backoff in your agent definition to ensure that transient network issues don't break your structural analysis pipeline.

Yes, you can enable tool approval for sensitive operations like `get_binding_sites` or `get_molecules`. This forces the agent to pause until you verify the proposed action.

Use the `get_uniprot_mapping` tool. The agent takes the UniProt accession as input and returns the corresponding PDB chains for your workflow.

The server retrieves only open-access PDB data. The communication is authenticated via your endpoint token, ensuring that only your authorized agents interact with the service.

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