EBI InterPro MCP Server for Claude DesktopGive Claude Desktop instant access to 16 tools to Get Cdd Entry, Get Clan, Get Entry, and more

Name: EBI InterPro
Price: 29 USD
Availability: InStock
Rating: 4.9 (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.

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The EBI InterPro 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.

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Classic Setup·json

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

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About EBI InterPro MCP Server

Connect to the InterPro API and access the world's most comprehensive resource for protein family, domain, and functional site classification.

Claude Desktop is the definitive way to connect EBI InterPro 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

Domain Classification — Retrieve detailed InterPro entry information including family/domain descriptions, GO terms, and member database cross-references
Multi-Database Access — Query entries from Pfam, CDD, SMART, Prosite, PANTHER, Gene3D, HAMAP, and more through a unified interface
Protein Annotation — Find all InterPro domains, families, and sites annotated on any UniProt protein
Structure Mapping — Discover PDB structures containing proteins that match specific InterPro entries
Taxonomic Distribution — Explore which organisms contain proteins matching a domain or family — essential for evolutionary biology
Proteome Coverage — Assess domain annotation coverage for complete proteomes
Clan Analysis — Navigate Pfam clan hierarchies to understand super-family relationships

The EBI InterPro 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 InterPro tools available for Claude Desktop

When Claude Desktop connects to EBI InterPro through Vinkius, your AI agent gets direct access to every tool listed below — spanning interpro, pfam, protein-domains, 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 cdd entry on EBI InterPro

CDD provides curated models for protein domain families and includes additional alignment and structure data. Use accessions like cd00001. Get CDD (Conserved Domain Database) entry details

get

Get clan on EBI InterPro

Returns clan accession, name, description, and member counts. Use Pfam clan accessions like CL0001. Get Pfam clan (super-family grouping) details

get

Get entry on EBI InterPro

Returns name, type (family, domain, homologous superfamily, repeat, site), description, Gene Ontology terms, member database cross-references, and literature count. Use accessions like IPR000001, IPR036291. Get InterPro entry metadata for a family or domain

get

Get entry proteins on EBI InterPro

Returns protein accessions, names, lengths, and source organisms. Useful for finding all members of a protein family across the UniProt database. Get all proteins matching an InterPro entry

get

Get entry structures on EBI InterPro

Returns PDB IDs, names, experiment types, and resolutions. Useful for finding structural representatives of a protein family or domain. Get all PDB structures matching an InterPro entry

get

Get entry taxonomy on EBI InterPro

Returns taxonomy nodes with names, ranks, and protein counts. This answers the evolutionary biology question "which organisms have this domain/family?" and is essential for understanding protein evolution and conservation. Get taxonomic distribution of an InterPro entry

get

Get pfam entry on EBI InterPro

Pfam is the most widely used protein domain database. Use accessions like PF00069 (kinase domain), PF00076 (RRM domain). Get Pfam domain or family details

get

Get protein on EBI InterPro

Returns the protein name, length, source organism, evidence level, fragment status, and counters for how many InterPro entries, Pfam domains, structures, and taxa are associated with it. Get protein details with all domain and family assignments

get

Get protein entries on EBI InterPro

This is the key tool for understanding "what domains does my protein have?" — the fundamental question in protein characterization. Get all InterPro entries matching a specific protein

get

Get proteome on EBI InterPro

Returns proteome ID, organism name, strain, reference status, and counters for associated entries and proteins. Use UniProt proteome IDs like UP000005640 (human). Get proteome details with domain coverage statistics

get

Get structure on EBI InterPro

Use a 4-character PDB ID like 1cbs or 4hhb. Get a PDB structure with mapped InterPro annotations

get

Get taxonomy on EBI InterPro

Returns the organism name, rank, lineage, number of children taxa, and counters for associated InterPro entries and proteins. Use IDs like 9606 (human), 10090 (mouse), 562 (E. coli). Get taxonomic node with entry and protein counts

list

List entry databases on EBI InterPro

Shows the number of entries in each database. Useful for understanding the scope of available domain and family annotations. List all InterPro member databases and entry counts

Search entries on EBI InterPro

Optionally filter by entry type: family, domain, homologous_superfamily, repeat, or site. Returns accessions, names, types, and protein/structure counts. Use queries like "kinase", "zinc finger", "immunoglobulin". Search InterPro entries by keyword and type

Search proteins on EBI InterPro

Returns UniProt accessions, names, lengths, organisms, and annotation counts. Use queries like "insulin", "hemoglobin", "BRCA1". Search proteins in InterPro by name or keyword

Search taxonomy on EBI InterPro

Returns taxon IDs, names, ranks, and annotation counts. Use queries like "human", "drosophila", "arabidopsis", "saccharomyces". Search taxonomy by organism name

Connect EBI InterPro to Claude Desktop via MCP

Follow these steps to wire EBI InterPro 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 InterPro

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

Why Use Claude Desktop with the EBI InterPro MCP Server

Claude Desktop by Anthropic provides unique advantages when paired with EBI InterPro 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 InterPro + Claude Desktop Use Cases

Practical scenarios where Claude Desktop combined with the EBI InterPro 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 InterPro in Claude Desktop

Ready-to-use prompts you can give your Claude Desktop agent to start working with EBI InterPro immediately.

"What domains and families does the human TP53 protein belong to?"

"Show me all member databases in InterPro and how many entries each has."

"Which organisms have the kinase domain PF00069?"

Troubleshooting EBI InterPro MCP Server with Claude Desktop

Common issues when connecting EBI InterPro 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 InterPro + Claude Desktop FAQ

Common questions about integrating EBI InterPro 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.