/interpro-database

name: "interpro-database"
description: "Query InterPro REST API for protein domain architecture, family classification, and member-DB integration. Search entries, retrieve a protein's domains, list family members, get taxonomic distribution, link to PDB. Unifies Pfam, PANTHER, PIRSF, PRINTS, PROSITE, SMART, CDD, NCBIfam. Use uniprot-protein-database for sequences; pdb-database for 3D structures."
license: "CC-BY-4.0"

InterPro Database

Overview

InterPro is the EBI's integrated protein family, domain, and functional site database. It consolidates signatures from 13 member databases (Pfam, PANTHER, PIRSF, PRINTS, PROSITE, SMART, CDD, NCBIfam, and others) into unified InterPro entries, each describing a homologous superfamily, domain, family, repeat, or conserved site. The REST API at `https://www.ebi.ac.uk/interpro/api/` is free and requires no authentication.

When to Use

• Identifying all domains and families present in a protein by UniProt accession (domain architecture)
• Searching for proteins that contain a specific domain or belong to a specific family
• Finding the taxonomic distribution of organisms that encode a given domain or family
• Cross-linking a domain to experimental 3D structures in the PDB
• Checking which source databases (Pfam, PANTHER, SMART, etc.) cover an InterPro entry
• Discovering InterPro entries by keyword (e.g., "kinase domain") when you do not yet know the accession
• For protein sequence retrieval, functional annotations (GO, pathways, active sites), and ID mapping use `uniprot-protein-database`
• For downloading domain-aligned sequences or building HMM profiles use `Pfam` directly; InterPro is the meta-layer

Prerequisites

• **Python packages**: `requests`, `pandas`, `matplotlib`
• **Data requirements**: UniProt accessions (e.g., `P04637`) or InterPro accessions (e.g., `IPR011009`)
• **Environment**: internet connection; no API key required
• **Rate limits**: no published hard limit; use `time.sleep(1.0)` between requests for batch queries; paginate with `?cursor=` or `?page_size=`

pip install requests pandas matplotlib

Quick Start

import requests

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

def interpro_get(path: str, params: dict = None) -> dict:
    """Send a GET request to the InterPro API and return parsed JSON."""
    r = requests.get(
        f"{INTERPRO_BASE}/{path}",
        params=params,
        headers={"Accept": "application/json"},
        timeout=30
    )
    r.raise_for_status()
    return r.json()

# Get domain architecture for TP53 (P04637)
# Note: `protein/uniprot/{acc}/` returns only {metadata}; the entries-per-protein
# data lives at `entry/interpro/protein/uniprot/{acc}/` and is keyed `results`.
data = interpro_get("entry/interpro/protein/uniprot/P04637/")
entries = data.get("results", [])
print(f"InterPro entries for TP53: {data.get('count')}  (this page: {len(entries)})")
for e in entries[:4]:
    m = e["metadata"]
    print(f"  {m['accession']}  {m['type']:<25}  {m['name']}")
# InterPro entries for TP53: 9
#   IPR002117  family                     p53 tumour suppressor family
#   IPR036674  homologous_superfamily     p53-like tetramerisation domain superfamily

Core API

Query 1: Entry Search

Search for InterPro entries by name keyword or fetch a specific entry by accession.

import requests

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

def search_entries(query: str, entry_type: str = None,
                   page_size: int = 20) -> list:
    """Search InterPro entries by keyword; optionally filter by type."""
    params = {"search": query, "page_size": page_size}
    if entry_type:
        params["type"] = entry_type   # family, domain, homologous_superfamily, repeat, site
    r = requests.get(
        f"{INTERPRO_BASE}/entry/interpro/",
        params=params,
        headers={"Accept": "application/json"},
        timeout=30
    )
    r.raise_for_status()
    return r.json().get("results", [])

hits = search_entries("serine kinase", entry_type="domain")
print(f"InterPro domain entries matching 'serine kinase': {len(hits)}")
for h in hits[:5]:
    m = h["metadata"]
    print(f"  {m['accession']}  {m['type']:<10}  {m['name']}")
# InterPro domain entries matching 'serine kinase': 8
#   IPR000719  domain    Protein kinase domain
#   IPR008271  domain    Serine/threonine/tyrosine kinase, active site

# Fetch a specific InterPro entry by accession
r = requests.get(
    f"{INTERPRO_BASE}/entry/interpro/IPR000719/",
    headers={"Accept": "application/json"},
    timeout=30
)
r.raise_for_status()
meta = r.json()["metadata"]
print(f"Accession    : {meta['accession']}")
print(f"Name         : {meta['name']}")
print(f"Type         : {meta['type']}")
print(f"Member DBs   : {list(meta.get('member_databases', {}).keys())}")
go_terms = meta.get("go_terms", [])
print(f"GO terms     : {[g['identifier'] for g in go_terms[:3]]}")
# Accession    : IPR000719
# Name         : Protein kinase domain
# Type         : domain
# Member DBs   : ['pfam', 'smart', 'cdd', 'ncbifam', 'panther']
# GO terms     : ['GO:0004672', 'GO:0005524', 'GO:0006468']

Query 2: Protein Domain Architecture

Retrieve all InterPro entries (domains, families, sites) matched in a protein by UniProt accession.

import requests

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

def get_protein_domain_architecture(uniprot_acc: str) -> dict:
    """Return all InterPro entry matches for a protein. Uses the
    `entry/interpro/protein/uniprot/{acc}/` endpoint, which returns
    {count, next, previous, results}. Each result has metadata + a
    nested `proteins[0].entry_protein_locations` for the per-protein match."""
    r = requests.get(
        f"{INTERPRO_BASE}/entry/interpro/protein/uniprot/{uniprot_acc}/",
        headers={"Accept": "application/json"},
        timeout=60
    )
    r.raise_for_status()
    return r.json()

data = get_protein_domain_architec