Query Interpro

InterPro Protein Domain Database

Query the InterPro REST API for protein domains, families, and functional sites.

When to Use

• User asks about domains in a protein
• User wants to know what family a protein belongs to
• User asks about functional sites or motifs
• User wants domain architecture visualization

How to Execute

import requests
import json

BASE_URL = "https://www.ebi.ac.uk/interpro/api"

# 1. Get protein annotation (domains/families for a UniProt ID)
def get_protein_domains(uniprot_id):
    url = f"{BASE_URL}/protein/uniprot/{uniprot_id}"
    r = requests.get(url, headers={"Accept": "application/json"})
    r.raise_for_status()
    return r.json()

# 2. Get InterPro entry details
def get_interpro_entry(interpro_id):
    url = f"{BASE_URL}/entry/interpro/{interpro_id}"
    r = requests.get(url, headers={"Accept": "application/json"})
    r.raise_for_status()
    return r.json()

# 3. Search InterPro by text
def search_interpro(query, max_results=10):
    url = f"{BASE_URL}/entry/interpro"
    params = {"search": query, "page_size": max_results}
    r = requests.get(url, params=params, headers={"Accept": "application/json"})
    r.raise_for_status()
    return r.json()

# 4. Get domain matches for a protein
def get_domain_matches(uniprot_id):
    url = f"{BASE_URL}/protein/uniprot/{uniprot_id}/entry/interpro"
    r = requests.get(url, headers={"Accept": "application/json"})
    r.raise_for_status()
    return r.json()

# Example: TP53 domains
domains = get_domain_matches("P04637")
for result in domains.get("results", []):
    meta = result.get("metadata", {})
    name = meta.get("name", "N/A")
    ipr_type = meta.get("type", "N/A")
    accession = meta.get("accession", "N/A")
    proteins = result.get("proteins", [])
    if proteins:
        locations = proteins[0].get("entry_protein_locations", [])
        for loc in locations:
            for frag in loc.get("fragments", []):
                start = frag.get("start", "?")
                end = frag.get("end", "?")
                print(f"{accession} ({ipr_type}): {name} [{start}-{end}]")

Entry Types

• domain — Structural/functional domain
• family — Protein family
• homologous_superfamily — Distant homologs
• repeat — Repeated motif
• site — Active/binding site

Follow-up Suggestions

• "Want me to compare domains across species?"
• "Should I map these domains onto the 3D structure?"
• "Want me to find other proteins with the same domain?"

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: cheatthegod
• Source: cheatthegod/BioHermes
• License: MIT

Install and usage instructions live in the source repository linked above.