EBI PDBe MCP Server for Claude DesktopGive Claude Desktop 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

Claude Desktop is Anthropic's native application for interacting with Claude AI models on macOS and Windows. It was the first consumer application to ship with built-in MCP support, making it the reference implementation for the Model Context Protocol standard.

Ask AI about this MCP Server for Claude Desktop

Open in ChatGPT Open in Claude Open in Perplexity

The EBI PDBe MCP Server for Claude Desktop 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

Classic Setup·json

{
  "mcpServers": {
    "ebi-pdbe": {
      // Your Vinkius token. get it at cloud.vinkius.com
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

RecommendedModern Approach — Zero Configuration

Vinkius Desktop App

The modern way to manage MCP Servers — no config files, no terminal commands. Install EBI PDBe and 4,000+ MCP Servers from a single visual interface.

Download Free Open SourceNo signup required

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.

Claude Desktop is the definitive way to connect EBI PDBe to your AI workflow. Add Vinkius Edge URL to your config, restart the app, and Claude immediately exposes all 16 tools in the chat interface. ask a question, Claude calls the right tool, and you see the answer. Zero code, zero context switching.

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 Claude Desktop 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 Claude Desktop

When Claude Desktop 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 Claude Desktop via MCP

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

Open Claude Desktop Settings

Go to Settings → Developer → Edit Config to open claude_desktop_config.json

Add the MCP Server

Paste the configuration above into the mcpServers section

Restart Claude Desktop

Close and reopen Claude Desktop to load the new server

Start using EBI PDBe

Look for the 🔌 icon in the chat. your 16 tools are now available

Why Use Claude Desktop with the EBI PDBe MCP Server

Claude Desktop by Anthropic provides unique advantages when paired with EBI PDBe through the Model Context Protocol.

Claude Desktop is the reference MCP client. it was designed alongside the protocol itself, ensuring the most complete and stable MCP implementation available

Zero-code configuration: add a server URL to a JSON file and Claude instantly discovers and exposes all available tools in the chat interface

Claude's extended thinking capability lets it reason through multi-step tool usage, chaining multiple API calls to answer complex questions

Enterprise-grade security with local config storage. your tokens never leave your machine, and connections go directly to Vinkius Edge network

EBI PDBe + Claude Desktop Use Cases

Practical scenarios where Claude Desktop combined with the EBI PDBe MCP Server delivers measurable value.

Interactive data exploration: ask Claude to query DNS records, look up WHOIS data, and cross-reference results in a single conversation

Ad-hoc security audits: type a domain name and let Claude enumerate subdomains, check DNS history, and flag configuration anomalies. all through natural language

Executive briefings: generate comprehensive domain intelligence reports by asking Claude to compile findings into a formatted summary

Learning and training: new team members can explore API capabilities conversationally without needing to read documentation

Example Prompts for EBI PDBe in Claude Desktop

Ready-to-use prompts you can give your Claude Desktop 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 Claude Desktop

Common issues when connecting EBI PDBe to Claude Desktop through Vinkius, and how to resolve them.

Server not appearing after restart

Ensure the JSON is valid (no trailing commas). Check the file path: ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\\Claude\\ (Windows).

Authentication error

Verify your Vinkius token is correct. Go to cloud.vinkius.com to regenerate it if needed.

Tools not showing in chat

Click the 🔌 icon at the bottom of the chat input. If it shows 0 tools, the server may still be connecting. wait a few seconds.

EBI PDBe + Claude Desktop FAQ

Common questions about integrating EBI PDBe MCP Server with Claude Desktop.

How does Claude Desktop discover MCP tools?

When Claude Desktop starts, it reads the claude_desktop_config.json file and connects to each configured MCP server. It calls the tools/list endpoint to fetch the schema for every available tool, then surfaces them as clickable options in the chat interface via the 🔌 icon.

What happens if the MCP server is temporarily unavailable?

Claude Desktop handles disconnections gracefully. if the server is unreachable at startup, the tools simply won't appear. Once the server becomes available again, restarting Claude Desktop will re-establish the connection. There is no timeout penalty or error loop.

Can I connect multiple MCP servers simultaneously?

Yes. You can add as many servers as you need in the mcpServers section of the config file. Each server appears as a separate tool provider, and Claude can use tools from multiple servers in a single conversation turn.

Is there a limit on the number of tools per server?

Claude Desktop can handle hundreds of tools per server. However, for optimal LLM performance, Vinkius servers are designed to expose focused, well-documented tool sets rather than overwhelming the model with too many options.

Does Claude Desktop support Streamable HTTP transport?

Yes. Claude Desktop supports both SSE (Server-Sent Events) and the newer Streamable HTTP transport that Vinkius uses. Simply provide the server URL. Claude auto-negotiates the transport protocol.

Explore More MCP Servers

View all →

Parsio

12 tools

Extract structured data from emails and PDFs automatically with AI-powered parsing templates that learn from your documents.

WooCommerce Order Status Reader

1 tools

This MCP gives your AI agent the ability to check the real-time status and tracking information of any WooCommerce order using an Order ID or a Customer Email. Perfect for automating "where is my order?" (WISMO) support queries.