EBI PDBe MCP Server for OpenAI Agents SDKGive OpenAI Agents SDK instant access to 16 tools to Get Assemblies, Get Binding Sites, Get Cofactors, and more

Name: EBI PDBe
Price: 29 USD
Availability: InStock
Rating: 5.0 (1 reviews)
Author: Vinkius

GDPR Free for Subscribers

The OpenAI Agents SDK enables production-grade agent workflows in Python. Connect EBI PDBe through Vinkius and your agents gain typed, auto-discovered tools with built-in guardrails. no manual schema definitions required.

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The EBI PDBe MCP Server for OpenAI Agents SDK is a standout in the The Unthinkable category — giving your AI agent 16 tools to work with, ready to go from day one.

Built for AI Agents by Vinkius

Vinkius delivers Streamable HTTP and SSE to any MCP client

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python

import asyncio
from agents import Agent, Runner
from agents.mcp import MCPServerStreamableHttp

async def main():
    # Your Vinkius token. get it at cloud.vinkius.com
    async with MCPServerStreamableHttp(
        url="https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    ) as mcp_server:

        agent = Agent(
            name="EBI PDBe Assistant",
            instructions=(
                "You help users interact with EBI PDBe. "
                "You have access to 16 tools."
            ),
            mcp_servers=[mcp_server],
        )

        result = await Runner.run(
            agent, "List all available tools from EBI PDBe"
        )
        print(result.final_output)

asyncio.run(main())

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About EBI PDBe MCP Server

Connect to the PDBe (Protein Data Bank in Europe) API and access the world's most comprehensive repository of experimentally determined 3D macromolecular structures.

The OpenAI Agents SDK auto-discovers all 16 tools from EBI PDBe through native MCP integration. Build agents with built-in guardrails, tracing, and handoff patterns. chain multiple agents where one queries EBI PDBe, another analyzes results, and a third generates reports, all orchestrated through Vinkius.

What you can do

Structure Summaries — Get titles, authors, deposition dates, resolution, and experimental methods for any PDB entry
Molecular Entities — Retrieve protein chains, nucleic acids, ligands, their sequences, source organisms, and gene names
Binding Sites & Ligands — Access ligand binding pocket residues, small molecule ligands with formulas and weights
Quality Assessment — Check resolution, R-factors, and overall quality scores for structure reliability
UniProt Mappings — Map between UniProt sequence positions and PDB residue numbers
Biological Assemblies — Understand quaternary structure — monomer, dimer, tetramer, or higher-order complexes
Structure Search — Full-text Solr search across 200+ PDB metadata fields
Publications — Find primary citations, PubMed IDs, and related structural studies

The EBI PDBe MCP Server exposes 16 tools through the Vinkius. Connect it to OpenAI Agents SDK in under two minutes — credentials fully managed, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.

All 16 EBI PDBe tools available for OpenAI Agents SDK

When OpenAI Agents SDK connects to EBI PDBe through Vinkius, your AI agent gets direct access to every tool listed below — spanning pdb, protein-structure, 3d-structures, and more. Every call runs in a secure, isolated environment with full audit visibility. Beyond a simple connection, you get real-time monitoring of agent activity, enterprise governance, and optimized token usage.

get

Get assemblies on EBI PDBe

Returns assembly IDs, composition (which entities and how many copies), preferred assembly flag, and form description. Critical for understanding whether a protein functions as a monomer, dimer, tetramer, or higher-order complex. Get biological assembly information (quaternary structure)

get

Get binding sites on EBI PDBe

Critical for drug discovery, molecular docking, and understanding protein-ligand interactions. Get ligand binding site residues and interactions

get

Get cofactors on EBI PDBe

Cofactors like heme, NAD+, FAD, and metal ions are essential for enzyme catalysis and protein function. Get cofactor and prosthetic group annotations

get

Get experiment on EBI PDBe

Get experimental method details for a structure

get

Get ligand monomers on EBI PDBe

Returns chemical component IDs, names, molecular formulas, molecular weights, and their chain/residue positions. Essential for drug discovery and understanding protein-small molecule interactions. Get small molecule ligands bound in the structure

get

Get modified residues on EBI PDBe

Shows the parent compound ID and modification name. Get non-standard amino acids and nucleotides

get

Get molecules on EBI PDBe

Returns entity IDs, molecule types, names, chain assignments, sequence lengths, molecular weights, source organisms, and gene names. Get molecular entities (chains, polymers) in a structure

get

Get mutated residues on EBI PDBe

Shows the original residue, mutated residue, chain, and position. Essential for understanding how the crystallized construct differs from the native protein. Get engineered mutations vs. wild-type sequence

get

Get publications on EBI PDBe

Useful for finding the primary citation and methodology papers for a structure. Get associated journal publications and PubMed IDs

get

Get quality scores on EBI PDBe

The first thing a structural biologist checks when evaluating a structure for reliability. Get global quality metrics for a structure

get

Get related entries on EBI PDBe

Useful for discovering alternative conformations, mutants, or complexes of the same protein that have been structurally characterized. Get related PDB entries citing the same publications

get

Get residue listing on EBI PDBe

Shows residue names, numbers (both PDB and author numbering), organized by entity and chain. Returns a sample of the first 20 residues per chain for efficiency. Get full residue-level inventory per chain

get

Get secondary structure on EBI PDBe

Shows the count of helices and strands per chain, organized by molecular entity. Essential for understanding protein fold topology. Get helix, sheet, and coil assignments per residue

get

Get summary on EBI PDBe

Use a 4-character PDB ID such as 1cbs, 4hhb, 6lu7. Get PDB entry summary with title, authors, and resolution

get

Get uniprot mapping on EBI PDBe

Returns UniProt accessions, chain assignments, and start/end position mappings. Essential for cross-referencing between protein sequence databases and 3D structural data. Get UniProt to PDB residue mappings

Search structures on EBI PDBe

Use natural language queries like "insulin receptor kinase", "SARS-CoV-2 spike protein", "cryo-EM resolution<3", or specific organism names. Returns PDB IDs, titles, methods, resolutions, and organisms. Search PDB structures with full-text queries

Connect EBI PDBe to OpenAI Agents SDK via MCP

Follow these steps to wire EBI PDBe into OpenAI Agents SDK. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.

Install the SDK

Run pip install openai-agents in your Python environment

Replace the token

Replace [YOUR_TOKEN_HERE] with your Vinkius token from cloud.vinkius.com

Run the script

Save the code above and run it: python agent.py

Explore tools

The agent will automatically discover 16 tools from EBI PDBe

Why Use OpenAI Agents SDK with the EBI PDBe MCP Server

OpenAI Agents SDK provides unique advantages when paired with EBI PDBe through the Model Context Protocol.

Native MCP integration via `MCPServerSse`, pass the URL and the SDK auto-discovers all tools with full type safety

Built-in guardrails, tracing, and handoff patterns let you build production-grade agents without reinventing safety infrastructure

Lightweight and composable: chain multiple agents and MCP servers in a single pipeline with minimal boilerplate

First-party OpenAI support ensures optimal compatibility with GPT models for tool calling and structured output

EBI PDBe + OpenAI Agents SDK Use Cases

Practical scenarios where OpenAI Agents SDK combined with the EBI PDBe MCP Server delivers measurable value.

Automated workflows: build agents that query EBI PDBe, process the data, and trigger follow-up actions autonomously

Multi-agent orchestration: create specialist agents. one queries EBI PDBe, another analyzes results, a third generates reports

Data enrichment pipelines: stream data through EBI PDBe tools and transform it with OpenAI models in a single async loop

Customer support bots: agents query EBI PDBe to resolve tickets, look up records, and update statuses without human intervention

Example Prompts for EBI PDBe in OpenAI Agents SDK

Ready-to-use prompts you can give your OpenAI Agents SDK agent to start working with EBI PDBe immediately.

"Show me the structure summary and quality of the SARS-CoV-2 main protease (6lu7)."

"What ligands are bound in the hemoglobin structure 4hhb?"

"Search for cryo-EM structures of ribosome complexes."

Troubleshooting EBI PDBe MCP Server with OpenAI Agents SDK

Common issues when connecting EBI PDBe to OpenAI Agents SDK through Vinkius, and how to resolve them.

MCPServerStreamableHttp not found

Ensure you have the latest version: pip install --upgrade openai-agents

Agent not calling tools

Make sure your prompt explicitly references the task the tools can help with.

EBI PDBe + OpenAI Agents SDK FAQ

Common questions about integrating EBI PDBe MCP Server with OpenAI Agents SDK.

How does the OpenAI Agents SDK connect to MCP?

Use MCPServerSse(url=...) to create a server connection. The SDK auto-discovers all tools and makes them available to your agent with full type information.

Can I use multiple MCP servers in one agent?

Yes. Pass a list of MCPServerSse instances to the agent constructor. The agent can use tools from all connected servers within a single run.

Does the SDK support streaming responses?

Yes. The SDK supports SSE and Streamable HTTP transports, both of which work natively with Vinkius.

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