# EBI InterPro MCP for AI Agents AI Agent Connect

> EBI InterPro lets you classify protein sequences into families, predict functional domains, and map evolutionary relationships. It connects your AI agent to the InterPro API, giving it the ability to query over 13 different databases like Pfam and SMART. Use it to find structural matches in PDB, see taxonomic distributions across species, or audit proteome coverage for your research.

## Overview
- **Category:** the-unthinkable
- **Price:** Free
- **Endpoint:** https://edge.vinkius.com/vk_preview_cBrAY2Gy2NSFguudqzcAnkyhKLGxzkfF44ThKH5h/ai-agent-connect
- **Tags:** interpro, pfam, protein-domains, protein-families, bioinformatics, embl-ebi, functional-annotation

## Description

You're looking for a way to turn your AI agent into a specialist for protein domain classification. This Connector handles the heavy lifting by connecting your agent directly to the InterPro API, which is the gold standard for protein family and functional site data. Instead of jumping between different databases like Pfam, CDD, or SMART, you can just ask your agent to do the work for you. It can pull together detailed entry info, find specific proteins matching an entry, or tell you which organisms actually contain a specific domain. It's a huge win for anyone who needs to move from a raw sequence to a functional understanding without manual searching. You can find this and thousands of other tools in the Vinkius catalog, making it easy to set up a biology-focused workflow in minutes. Your agent can then help you map out evolutionary patterns or find 3D structures that match your protein of interest. It's about getting answers to what does this do and where does it exist without the manual overhead of navigating multiple web portals.

## Tools

### get_entry_taxonomy
See which organisms contain a specific domain to understand its evolutionary conservation. Returns taxonomy nodes and counts.

### get_cdd_entry
Get curated models and alignment data for conserved domain families. Use this for detailed CDD entry information.

### get_entry_proteins
List all proteins in the UniProt database that match a specific InterPro entry. Useful for finding family members.

### get_protein_entries
Identify every InterPro domain and family associated with a specific protein. This is the core tool for protein characterization.

### get_clan
Pull accession details and member counts for Pfam super-family groupings. This helps understand clan hierarchies.

### get_entry
Retrieve metadata like GO terms and literature counts for a specific family or domain. Use this for general entry info.

### get_entry_structures
Find all PDB structures that contain a specific protein family or domain. This helps locate structural representatives.

### get_pfam_entry
Fetch specific domain or family details from the Pfam database. Use this for the most widely used protein domain data.

### get_protein
Get a summary of a protein's name, length, and all its associated domain assignments. Provides a high-level protein overview.

### get_proteome
Check domain coverage statistics and metadata for a specific UniProt proteome. Use this for large-scale proteome analysis.

### get_structure
Pull a specific PDB structure with its mapped InterPro annotations. Use a 4-character PDB ID to get mapped data.

### get_taxonomy
Get the lineage and protein counts for a specific taxonomic node. Use this to explore organism-specific protein counts.

### list_entry_databases
See a list of all member databases and their entry counts. Use this to understand the scope of the InterPro integration.

### search_entries
Search for InterPro entries using keywords like kinase or zinc finger. Filter by entry type to find specific domains.

### search_proteins
Find UniProt proteins by name or keyword to see their domain assignments. Great for finding specific proteins in the database.

### search_taxonomy
Search for specific organisms by name to see their associated protein counts. Use this to find taxonomy IDs quickly.

## Prompt Examples

**Prompt:** 
```
What domains and families does the human TP53 protein belong to?
```

**Response:** 
```
I've retrieved all InterPro annotations for TP53 (P04637). The protein is classified into the p53 tumor suppressor family (IPR002117) and contains several key domains:

* **p53 DNA-binding domain** (IPR011615)
* **p53 tetramerization domain** (IPR010991)
* **Transactivation domain**

These domains are conserved across vertebrates and define the functional architecture of p53 as a transcription factor.
```

**Prompt:** 
```
Show me all member databases in InterPro and how many entries each has.
```

**Response:** 
```
The InterPro platform integrates 13+ member databases. Here is a breakdown of the scope:

| Database | Key Features |
| :--- | :--- |
| **Pfam** | 20,000+ families and domains |
| **PANTHER** | Protein families and domains |
| **CDD** | Conserved Domain Database |
| **SMART** | Signature and motifs |

Other members include Gene3D, HAMAP, Prosite, PRINTS, PIRSF, SFLD, NCBIfam, and AntiFam.
```

**Prompt:** 
```
Which organisms have the kinase domain PF00069?
```

**Response:** 
```
The protein kinase domain (Pfam PF00069) is integrated into InterPro as IPR000719. 

**Taxonomic Distribution:**
This domain is universally conserved across all kingdoms of life, including:
* **Bacteria**
* **Archaea**
* **Plants**
* **Fungi**
* **Animals**

The human genome alone contains hundreds of proteins with this domain, making it one of the most expanded families in eukaryotic evolution.
```

## Capabilities

### Identify protein domains
Get specific functional site info and family descriptions for any protein sequence.

### Map taxonomic distributions
See which organisms have specific domains to study their evolutionary conservation.

### Find structural matches
Locate PDB structures that contain specific protein families or domains.

### Analyze Pfam clans
Understand super-family relationships by navigating Pfam clan hierarchies.

### Query multi-database entries
Search Pfam, CDD, SMART, and more through a single unified interface.

### Audit proteome coverage
Assess domain annotation coverage for complete proteomes across different species.

## Use Cases

### Identifying domains in a new protein
A molecular biologist wants to know what domains are in a new protein. They ask the agent to find all assignments for a specific UniProt ID.

### Mapping evolutionary conservation
An evolutionary biologist needs to see if a domain is universal. They use get_entry_taxonomy to check distribution across kingdoms.

### Locating structural models
A structural biologist needs a 3D model of a kinase. They use get_entry_structures to find relevant PDB IDs.

### Broad database exploration
A bioinformatician is building a pipeline. They use list_entry_databases to see the scope of available data.

## Benefits

- You can skip manual database jumping because this Connector queries Pfam, CDD, and SMART in one place.
- You'll find 3D structures faster by using get_entry_structures to link families to PDB IDs.
- You can map evolutionary history quickly with get_entry_taxonomy to see domain distribution.
- You'll get better protein characterization by pulling all assignments at once with get_protein_entries.
- You can audit entire proteomes for domain coverage using get_proteome to see what's missing.
- You'll simplify your research by using search_entries to find keywords across multiple databases simultaneously.

## How It Works

The bottom line is you get a protein domain expert inside your AI client with zero configuration.

1. Subscribe to the EBI InterPro MCP on Vinkius.
2. Connect your AI client to the Connector without needing any API keys.
3. Ask your agent to classify proteins, find structures, or map evolutionary data.

## Frequently Asked Questions

**Can the EBI InterPro MCP help me identify protein functions?**
Yes, it lets you see the functional domains and families assigned to a protein. This helps you understand what a protein actually does in a cell.

**Does this Connector work with Pfam and SMART?**
Yes, it pulls data from over 13 databases including Pfam, SMART, and CDD. You get a unified view of all these resources.

**Can I use EBI InterPro to find 3D structures?**
You can use it to find PDB structures that contain specific protein domains. This is great for finding structural examples of a family.

**How does EBI InterPro help with evolutionary biology?**
It provides taxonomic distribution for protein domains. You can see which organisms have specific domains to study their evolution.

**Do I need an API key for EBI InterPro?**
No, the InterPro API is public, so you can start using this Connector immediately after connecting it to your agent.

**Can I search for proteins by keyword?**
Yes, you can search for proteins by name or keyword to see their domain assignments. It's a fast way to explore specific protein types.

**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.