interpro-database

InterPro Database

Overview

InterPro (https://www.ebi.ac.uk/interpro/) is a comprehensive resource for protein family and domain classification maintained by EMBL-EBI. It integrates signatures from 13 member databases including Pfam, PANTHER, PRINTS, ProSite, SMART, TIGRFAM, SUPERFAMILY, CDD, and others, providing a unified view of protein functional annotations for over 100 million protein sequences.

InterPro classifies proteins into:

• Families: Groups of proteins sharing common ancestry and function
• Domains: Independently folding structural/functional units
• Homologous superfamilies: Structurally similar protein regions
• Repeats: Short tandem sequences
• Sites: Functional sites (active, binding, PTM)

Key resources:

• InterPro website: https://www.ebi.ac.uk/interpro/
• REST API: https://www.ebi.ac.uk/interpro/api/
• API documentation: https://github.com/ProteinsWebTeam/interpro7-api/blob/master/docs/
• Python client: via requests

When to Use This Skill

Use InterPro when:

• Protein function prediction: What function(s) does an uncharacterized protein likely have?
• Domain architecture: What domains make up a protein, and in what order?
• Protein family classification: Which family/superfamily does a protein belong to?
• GO term annotation: Map protein sequences to Gene Ontology terms via InterPro
• Evolutionary analysis: Are two proteins in the same homologous superfamily?
• Structure prediction context: What domains should a new protein structure be compared against?
• Pipeline annotation: Batch-annotate proteomes or novel sequences

Core Capabilities

1. InterPro REST API

Base URL: https://www.ebi.ac.uk/interpro/api/

import requests

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

def interpro_get(endpoint, params=None):
    url = f"{BASE_URL}/{endpoint}"
    headers = {"Accept": "application/json"}
    response = requests.get(url, params=params, headers=headers)
    response.raise_for_status()
    return response.json()