How to Use the EBI PDBe MCP in Vercel AI SDK

Q: How do I search the EBI PDBe database using the Vercel AI SDK?

You invoke the searchstructures tool within your agent's execution flow. Pass your query string as an argument, and the server returns a list of relevant PDB entries.

Q: Does the EBI PDBe integration expose ligand data to my Vercel AI SDK app?

It does. You can call getligandmonomers or getbindingsites to extract chemical component details and interaction data for any valid PDB ID.

Stream EBI PDBe structural data directly into your Vercel AI SDK interface for real-time molecular visualization.

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Connect EBI PDBe MCP to Vercel AI SDK

Create your Vinkius account to connect EBI PDBe to Vercel AI SDK 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 Vercel AI SDK

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Instant structural data retrieval

Feed your UI with live PDB entry summaries. Use `get_summary` to pull in resolution, author lists, and experimental methods the moment a user requests a protein ID. Your application renders this data instantly. The Vercel AI SDK handles the stream, so your user sees the structural details appear without waiting for a backend process.

Map residues with MCP Server tools

Connect your frontend to UniProt mappings using `get_uniprot_mapping`. This MCP Server bridges the gap between sequence databases and 3D coordinate space. You avoid manual lookups. The AI client resolves the cross-reference, and your UI updates with the exact residue range for the queried chain.

Search structures via natural language

Execute `search_structures` to filter the entire Protein Data Bank using simple phrases. Your agent parses the request and retrieves matching IDs for cryo-EM or X-ray structures. It returns the core metadata needed to populate your search results. You get the PDB ID, title, and organism directly in the client response.

Setup guide

Set up EBI PDBe MCP in Vercel AI SDK

Prerequisites

Node.js 18+ and a TypeScript project
ai + @modelcontextprotocol/sdk packages
Active Vinkius subscription with a valid endpoint token

1

Install dependencies

Run npm install ai @modelcontextprotocol/sdk plus your preferred model provider (e.g. @ai-sdk/openai).
2

Create the Streamable HTTP transport

Use StreamableHTTPClientTransport with your Vinkius endpoint URL. Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com.
3

Discover and use tools

Call mcpClient.tools() to auto-discover all EBI PDBe tools. Pass them directly to generateText() or streamText() — no manual schema definitions needed.
4

Works with any model provider

Swap openai("gpt-4o") for any AI SDK provider — Anthropic, Google, Mistral. The MCP tools work identically across all supported models.

index.ts

import { experimental_createMCPClient as createMCPClient } from "ai";
import { StreamableHTTPClientTransport } from "@modelcontextprotocol/sdk/client/streamableHttp";
import { generateText } from "ai";
import { openai } from "@ai-sdk/openai";

const transport = new StreamableHTTPClientTransport(
  new URL("https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp")
);

const mcpClient = await createMCPClient({ transport });
const tools = await mcpClient.tools();

const { text } = await generateText({
  model: openai("gpt-4o"),
  tools,
  prompt: "List recent EBI PDBe transactions",
});

console.log(text);
await mcpClient.close();

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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 Vercel AI SDK

You invoke the `search_structures` tool within your agent's execution flow. Pass your query string as an argument, and the server returns a list of relevant PDB entries.

Yes, but keep an eye on your API limits. The server is designed for efficient data fetching, though you should implement caching if your UI performs frequent updates.

It does. You can call `get_ligand_monomers` or `get_binding_sites` to extract chemical component details and interaction data for any valid PDB ID.

The server returns an error message indicating the ID was not found. Your agent logic should catch this response and prompt the user for a correct identifier.

The server only processes public structural data from the Protein Data Bank. No private user information is ever transmitted or stored during these requests.

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