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EBI InterPro

EBI InterPro MCP for AI. Classify proteins down to their functional domains.

Claude Claude
ChatGPT ChatGPT
Cursor Cursor
Gemini Gemini
Windsurf Windsurf
VS Code VS Code
JetBrains JetBrains
Vercel Vercel
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EBI InterPro MCP on Cursor AI Code EditorEBI InterPro MCP on Claude Desktop AppEBI InterPro MCP on OpenAI Agents SDKEBI InterPro MCP on Visual Studio CodeEBI InterPro MCP on GitHub Copilot AI AgentEBI InterPro MCP on Google Gemini AIEBI InterPro MCP on Lovable AI DevelopmentEBI InterPro MCP on Mistral AI AgentsEBI InterPro MCP on Amazon AWS Bedrock

Connect to your AI in seconds.

EBI InterPro MCP connects your AI agent to the world's central resource for protein classification. This MCP allows you to classify proteins by predicting functional domains, mapping structural data, and exploring evolutionary relationships across every species.

It lets you go beyond simple sequence matching, giving deep insight into a protein's function based on its domain profile.

What your AI can do

Get cdd entry

Retrieves detailed information about a specific Conserved Domain Database (CDD) entry using an accession number.

Get clan

Gets super-family grouping details for Pfam clans, including the name and member count of the group.

Get entry

Fetches general metadata for any InterPro entry, listing its family type, GO terms, and cross-references to other databases.

+ 13 more capabilities included
Classify protein domains

Predicts and retrieves detailed information about known functional domains (like Pfam or CDD) associated with a given protein sequence.

Map structural data

Finds specific PDB IDs and resolutions for proteins that match an InterPro entry, connecting function to physical structure.

Trace evolutionary lineage

Determines which organisms or taxonomic groups contain a protein matching a specific domain or family. This helps map evolution across life.

Identify proteome coverage gaps

Assesses how completely the proteins of an entire organism (a proteome) are annotated with known domains.

Retrieve all protein members

Lists every known protein in a database that shares a specific domain or family annotation, across different organisms.

Included with Plan

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AI Agent

EBI InterPro: 16 Tools for Bioinformatics

These tools let you search protein families, retrieve domain details, check taxonomy, or map structures using specific accessions and keywords.

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Get Cdd Entry

Retrieves detailed information about a specific Conserved Domain Database (CDD) entry using an accession number.

Get Clan

Gets super-family grouping details for Pfam clans, including the name and member...

Get Entry

Fetches general metadata for any InterPro entry, listing its family type, GO terms...

Get Entry Proteins

Returns a list of all protein accessions that match a given InterPro entry across...

Get Entry Structures

Finds all PDB structures associated with an InterPro entry, giving names and...

Get Entry Taxonomy

Returns the taxonomic distribution of an InterPro entry, showing which organisms contain that specific domain or family.

Get Pfam Entry

Gets detailed information for a Pfam domain or family using its accession number (e.g., PF00069).

Get Protein

Retrieves comprehensive details for a protein, including counts of associated...

Get Protein Entries

Lists every single InterPro entry that matches a specific protein sequence, which is...

Get Proteome

Gets domain coverage statistics and basic details for an entire organism's proteome...

Get Structure

Retrieves a PDB structure file along with mapped InterPro annotations based on a...

Get Taxonomy

Returns the taxonomic node details for an organism, including its rank and counts of associated entries and proteins.

List Entry Databases

Lists all member databases supported by InterPro and shows how many total entries each one contains.

Search Entries

Searches across InterPro entries using keywords (like 'kinase') or filtering by...

Search Proteins

Searches for proteins within InterPro using a name or keyword, giving back UniProt...

Search Taxonomy

Searches the organism database by common names (like 'human') to find relevant taxon...

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Claude AI

Claude AI

1

Open Claude Settings

Go to claude.ai, click your profile icon, then navigate to Customize → Connectors.

2

Add Custom Connector

Click the "+" button and select Add custom connector. Paste your Vinkius endpoint URL:

https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com. For OAuth-protected servers, expand Advanced settings to add credentials.

3

Start a conversation

Open a new chat. The EBI InterPro integration is available immediately — no restart needed.

Choose How to Get Started

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Start with EBI InterPro, then connect any of our 5,100+ other servers whenever your AI needs more. One click, no limits.

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Works with Claude, ChatGPT, Cursor, and more

The Model Context Protocol standardizes how applications expose capabilities to LLMs. Instead of operating in isolation, your AI gains direct access to external platforms, live data, and real-world actions through secure, standardized connections.

This connection provides 16 powerful capabilities that interface natively with Claude, ChatGPT, Cursor, and other compatible AI platforms. No middleware. No custom integration required.

Tracking protein function requires jumping between three different websites.

Today, if a bioinformatician wants to know about a domain, they first have to find the basic entry (Site A). Then they copy that ID and paste it into the structure database (Site B) to see PDBs. Finally, they jump over to the phylogeny site (Site C) just to check which species use it. It's slow, prone to copy-paste errors, and you lose context every time.

With this MCP, your agent handles all that hand-off for you. You ask one question—like 'What are the structures and species of this kinase domain?'—and get a single, unified report combining data from multiple sources. It's instant.

Get Domain Context with InterPro

The MCP automatically pulls in the deep details you used to spend hours collecting: it gathers the domain family descriptions, lists all related UniProt proteins via `get_entry_proteins`, and even maps out the full taxonomy using `get_entry_taxonomy`.

What changes is that your analysis moves from being a tedious data assembly job to a rapid question-and-answer session. You get the answer, not a list of links.

What your AI can actually do with this

This connector gives your agent the ability to analyze proteins at a highly technical level. You can feed it a protein sequence, and it will tell you exactly what functional domains that sequence belongs to—whether those are kinase domains or something else entirely. It pulls data from a huge collection of databases like Pfam and CDD through one unified interface.

Need to know which species carry this domain? Or where the 3D structure exists in the PDB archive? The MCP finds it all. You can even check how well an entire organism's proteome is annotated for domains, giving you a full picture of its functional coverage. Because Vinkius hosts this resource, your AI client treats InterPro like a single, massive domain expert, making complex biological questions easy to ask.

Built · Hosted · Managed by Vinkius InterPro MCP - Classify Protein Domains & Families
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Questions you might have

How do I find all domains for one protein using get_protein_entries? +

You pass the UniProt accession to get_protein_entries. It returns every associated InterPro entry, giving you a complete list of its functional domain assignments.

Can I use search_taxonomy to find an organism's full profile? +

Yes. You run search_taxonomy with the name (e.g., 'human'), and then use get_taxonomy on the returned ID to get its rank, lineage, and associated protein counts.

What is the difference between get_protein and get_proteome? +

get_protein gives you domain data for a single sequence. get_proteome looks at an entire organism's ID, providing stats on how many proteins in that whole genome are annotated with domains.

How do I check if Pfam is included in the database scope? Use list_entry_databases. +

Running list_entry_databases shows you all member databases. You'll see Pfam listed there, along with its current entry count, confirming it's part of the unified resource.

When using `search_entries`, how should I filter my results to look only at domains, excluding entire families? +

You must specify the entry type parameter in search_entries. This allows you to narrow the search scope immediately. Instead of getting all related data, you limit the output strictly to domain or family types as needed for your analysis.

If I run `get_entry` for an InterPro ID, how do I use `get_entry_structures` to find its associated 3D models? +

You pass the primary InterPro accession ID into get_entry_structures. This function links the abstract annotation metadata directly to physical structural data. It returns PDB IDs and resolution details for comparison.

When I use `get_taxonomy`, how do I explore the evolutionary lineage or parent nodes of an organism? +

The get_taxonomy tool includes rank information in its results. This lets you trace ancestry and see which broader groups contain a specific species ID. It maps hierarchical relationships, essential for understanding conservation.

Can I use `get_pfam_entry` to query multiple Pfam accessions (like PF00069 and another one) in a single request? +

Yes. The tool accepts an array or comma-separated list of Pfam IDs for batch querying. This is the most efficient way to retrieve domain details for several known protein families at once.

Do I need an API key? +

No. The InterPro API is completely public and requires no authentication. Enter any placeholder value in the API key field to activate the server immediately.

What databases does InterPro integrate? +

InterPro integrates 13+ member databases including Pfam (protein families), CDD (conserved domains from NCBI), SMART (signalling domains), Prosite (patterns and profiles), PANTHER (evolutionary classification), Gene3D (structural domains from CATH), HAMAP (microbial families), PRINTS (fingerprints), PIRSF (classification system), SFLD (superfamilies), and NCBIfam. This gives you a unified view of protein domain and family annotations from the world's leading classification resources.

Can I find which organisms have a specific protein domain? +

Yes. Use the get_entry_taxonomy tool with any InterPro accession to see the taxonomic distribution of that domain or family. This shows which organisms — from bacteria to humans — contain proteins with that specific domain. It is one of the most powerful tools for evolutionary biology, revealing how protein domains have been conserved or diversified across the tree of life.

Built & Managed by Vinkius 30s setup 16 tools

We've already built the connector for EBI InterPro. Just plug in your AI agents and start using Vinkius.

No hosting. No infrastructure. No complex setup.
All 16 tools are live and waiting. You're up and running in seconds.

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