EBI PDBe MCP Server for Pydantic AIGive Pydantic AI 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

Pydantic AI brings type-safe agent development to Python with first-class MCP support. Connect EBI PDBe through Vinkius and every tool is automatically validated against Pydantic schemas. catch errors at build time, not in production.

Ask AI about this MCP Server for Pydantic AI

Open in ChatGPT Open in Claude Open in Perplexity

The EBI PDBe MCP Server for Pydantic AI 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

Claude

ChatGPT

Cursor

Gemini

Windsurf

VS Code

JetBrains

Vercel

+ other MCP clients

python

import asyncio
from pydantic_ai import Agent
from pydantic_ai.mcp import MCPServerHTTP

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

    agent = Agent(
        model="openai:gpt-4o",
        mcp_servers=[server],
        system_prompt=(
            "You are an assistant with access to EBI PDBe "
            "(16 tools)."
        ),
    )

    result = await agent.run(
        "What tools are available in EBI PDBe?"
    )
    print(result.data)

asyncio.run(main())

Fully ManagedVinkius Servers

60%Token savings

High SecurityEnterprise-grade

IAMAccess control

EU AI ActCompliant

DLPData protection

V8 IsolateSandboxed

Ed25519Audit chain

<40msKill switch

Stream every event to Splunk, Datadog, or your own webhook in real-time

* Every MCP server runs on Vinkius-managed infrastructure inside AWS - a purpose-built runtime with per-request V8 isolates, Ed25519 signed audit chains, and sub-40ms cold starts optimized for native MCP execution. See our infrastructure

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.

Pydantic AI validates every EBI PDBe tool response against typed schemas, catching data inconsistencies at build time. Connect 16 tools through Vinkius and switch between OpenAI, Anthropic, or Gemini without changing your integration code. full type safety, structured output guarantees, and dependency injection for testable agents.

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 Pydantic AI 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 Pydantic AI

When Pydantic AI 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 Pydantic AI via MCP

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

Install Pydantic AI

Run pip install pydantic-ai

Replace the token

Replace [YOUR_TOKEN_HERE] with your Vinkius token

Run the agent

Save to agent.py and run: python agent.py

Explore tools

The agent discovers 16 tools from EBI PDBe with type-safe schemas

Why Use Pydantic AI with the EBI PDBe MCP Server

Pydantic AI provides unique advantages when paired with EBI PDBe through the Model Context Protocol.

Full type safety: every MCP tool response is validated against Pydantic models, catching data inconsistencies before they reach your application

Model-agnostic architecture. switch between OpenAI, Anthropic, or Gemini without changing your EBI PDBe integration code

Structured output guarantee: Pydantic AI ensures tool results conform to defined schemas, eliminating runtime type errors

Dependency injection system cleanly separates your EBI PDBe connection logic from agent behavior for testable, maintainable code

EBI PDBe + Pydantic AI Use Cases

Practical scenarios where Pydantic AI combined with the EBI PDBe MCP Server delivers measurable value.

Type-safe data pipelines: query EBI PDBe with guaranteed response schemas, feeding validated data into downstream processing

API orchestration: chain multiple EBI PDBe tool calls with Pydantic validation at each step to ensure data integrity end-to-end

Production monitoring: build validated alert agents that query EBI PDBe and output structured, schema-compliant notifications

Testing and QA: use Pydantic AI's dependency injection to mock EBI PDBe responses and write comprehensive agent tests

Example Prompts for EBI PDBe in Pydantic AI

Ready-to-use prompts you can give your Pydantic AI 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 Pydantic AI

Common issues when connecting EBI PDBe to Pydantic AI through Vinkius, and how to resolve them.

MCPServerHTTP not found

Update: pip install --upgrade pydantic-ai

EBI PDBe + Pydantic AI FAQ

Common questions about integrating EBI PDBe MCP Server with Pydantic AI.

How does Pydantic AI discover MCP tools?

Create an MCPServerHTTP instance with the server URL. Pydantic AI connects, discovers all tools, and generates typed Python interfaces automatically.

Does Pydantic AI validate MCP tool responses?

Yes. When you define result types as Pydantic models, every tool response is validated against the schema. Invalid data raises a clear error instead of silently corrupting your pipeline.

Can I switch LLM providers without changing MCP code?

Absolutely. Pydantic AI abstracts the model layer. your EBI PDBe MCP integration works identically with OpenAI, Anthropic, Google, or any supported provider.