🧬 InterPro Protein Families Scraper

🚀 Export protein family and domain entries from InterPro in one run. Pull from a catalog of more than 51,000 entries across the EBI InterPro database.

🕒 Last updated: 2026-06-08 · 📊 20 fields per record · 8 entry types · live EBI InterPro API

Turn the EBI InterPro classification database into clean, structured records you can drop into a bioinformatics pipeline, a functional annotation table, or a protein research notebook. Fetch specific accessions like IPR000001, or browse the full catalog and narrow it to a single entry type such as family or domain.

Coverage is the complete public InterPro entry set as the EMBL-EBI InterPro API publishes it: every entry with its accession, type, name, integrated member database signatures from Pfam, SMART, CDD, PANTHER and more, Gene Ontology terms, overlapping superfamilies, and live counts of matching proteins, structures, taxa, and pathways.

🎯 Target Audience	💡 Primary Use Cases
Bioinformaticians and computational biologists	Annotate proteins with family and domain assignments
Database and tool builders	Seed a local copy of the InterPro classification
Protein and structural biology researchers	Map signatures, GO terms, and overlapping superfamilies
Data scientists in life sciences	Build feature tables from family membership and counts

📋 What the InterPro Protein Families Scraper does

This Actor calls the public EBI InterPro REST API and returns one clean record per entry:

• By accession — provide a list of InterPro accessions and get exactly those entries with full detail.
• Browse all — leave the accession list empty to walk the whole catalog, optionally filtered to one entry type.

Each record carries the entry accession, type, name, short name, member database signatures, GO terms, overlapping superfamilies, a cleaned text description, live counters, and a scrapedAt timestamp.

🎬 Full Demo (🚧 Coming soon)

⚙️ Input

Field	Type	Description
accessions	array	Optional list of InterPro accessions to fetch, for example IPR000001. When non-empty, the Actor fetches exactly these entries and ignores the type filter.
type	select	Used only when no accessions are given. Restricts browsing to one entry type. One of family, domain, homologous_superfamily, repeat, conserved_site, active_site, binding_site, ptm, or any.
maxItems	integer	How many records to return. Free plan is capped at 10.

Example 1 — fetch specific accessions

{
    "accessions": ["IPR000001", "IPR000003", "IPR000006"],
    "maxItems": 10
}

Example 2 — browse all families

{
    "type": "family",
    "maxItems": 100
}

⚠️ Good to Know: The InterPro catalog holds more than 51,000 entries. When browsing, set maxItems to the slice you actually need. Browsing fetches each entry's full detail page, so larger runs take longer than a flat list.

📊 Output

Each record looks like this:

Field	Description
🧬 accession	InterPro accession (stable ID)
📌 name	Entry name
🏷 type	Entry type (family, domain, etc.)
🔗 url	InterPro entry page URL
✂️ shortName	Short machine-friendly name
🗄 sourceDatabase	Source database (interpro)
📝 description	Cleaned text description
🗂 memberDatabaseList	Member databases that contribute signatures
🔢 memberDatabaseCount	Number of member databases
🧩 signaturesCount	Number of integrated signatures
🧩 signatures	Array of signatures (database, accession, name)
🔬 goTermsCount	Number of GO terms
🔬 goTerms	Array of GO terms (identifier, name, category)
🔁 overlapsWith	Overlapping entries (accession, name, type)
👥 proteinCount	Matching proteins
🧱 structureCount	Matching structures
🌳 taxaCount	Matching taxa
🛤 pathwayCount	Linked pathways
🕒 scrapedAt	Collection timestamp
❌ error	Null on success

Real sample — domain

{
    "accession": "IPR000001",
    "name": "Kringle",
    "type": "domain",
    "url": "https://www.ebi.ac.uk/interpro/entry/InterPro/IPR000001/",
    "shortName": "Kringle",
    "sourceDatabase": "interpro",
    "description": "Kringles are autonomous structural domains, found throughout the blood clotting and fibrinolytic proteins...",
    "memberDatabaseList": ["cdd", "profile", "pfam", "smart"],
    "memberDatabaseCount": 4,
    "signaturesCount": 4,
    "signatures": [
        { "database": "cdd", "accession": "cd00108", "name": "KR" },
        { "database": "pfam", "accession": "PF00051", "name": "Kringle domain" },
        { "database": "smart", "accession": "SM00130", "name": "Kringle domain" }
    ],
    "goTermsCount": 0,
    "goTerms": [],
    "overlapsWith": [
        { "accession": "IPR038178", "name": "Kringle superfamily", "type": "homologous_superfamily" },
        { "accession": "IPR013806", "name": "Kringle-like fold", "type": "homologous_superfamily" }
    ],
    "proteinCount": 21741,
    "structureCount": 134,
    "taxaCount": 4840,
    "pathwayCount": 131,
    "scrapedAt": "2026-06-08T18:39:40.638Z",
    "error": null
}

Real sample — family with GO terms

{
    "accession": "IPR000003",
    "name": "Retinoid X receptor/HNF4",
    "type": "family",
    "url": "https://www.ebi.ac.uk/interpro/entry/InterPro/IPR000003/",
    "shortName": "Retinoid-X_rcpt/HNF4",
    "sourceDatabase": "interpro",
    "description": "Steroid or nuclear hormone receptors (NRs) constitute an important superfamily of transcription regulators...",
    "memberDatabaseList": ["prints"],
    "memberDatabaseCount": 1,
    "signaturesCount": 1,
    "signatures": [
        { "database": "prints", "accession": "PR00545", "name": "Retinoid X receptor" }
    ],
    "goTermsCount": 5,
    "goTerms": [
        { "identifier": "GO:0003677", "name": "DNA binding", "category": "molecular_function" },
        { "identifier": "GO:0005634", "name": "nucleus", "category": "cellular_component" }
    ],
    "overlapsWith": [
        { "accession": "IPR013088", "name": "Zinc finger, NHR/GATA-type", "type": "homologous_superfamily" }
    ],
    "proteinCount": 8170,
    "structureCount": 127,
    "taxaCount": 4458,
    "pathwayCount": 85,
    "scrapedAt": "2026-06-08T18:39:40.810Z",
    "error": null
}

Real sample — family

{
    "accession": "IPR000006",
    "name": "Metallothionein, vertebrate",
    "type": "family",
    "url": "https://www.ebi.ac.uk/interpro/entry/InterPro/IPR000006/",
    "shortName": "Metalthion_vert",
    "sourceDatabase": "interpro",
    "description": "Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel...",
    "memberDatabaseList": ["panther", "pfam", "prints"],
    "memberDatabaseCount": 3,
    "signaturesCount": 3,
    "signatures": [
        { "database": "panther", "accession": "PTHR23299", "name": "METALLOTHIONEIN" },
        { "database": "pfam", "accession": "PF00131", "name": "Metallothionein" }
    ],
    "goTermsCount": 1,
    "goTerms": [
        { "identifier": "GO:0046872", "name": "metal ion binding", "category": "molecular_function" }
    ],
    "overlapsWith": [
        { "accession": "IPR017854", "name": "Metallothionein domain superfamily", "type": "homologous_superfamily" }
    ],
    "proteinCount": 2444,
    "structureCount": 14,
    "taxaCount": 2186,
    "pathwayCount": 9,
    "scrapedAt": "2026-06-08T18:39:40.939Z",
    "error": null
}

✨ Why choose this Actor

• One clean record per entry, with the stable accession placed first for instant lookup.
• Two modes in one Actor, so accession lookups and full browsing share a consistent shape.
• Member database signatures and GO terms come fully expanded, not as bare nested blobs.
• No account, no key, and no login required.
• Stable field names that map cleanly onto a database schema.

📈 How it compares to alternatives

Approach	Effort	Structured fields	Counts included	Maintenance
This Actor	One run	Yes	Yes	None on your side
Hand-copying from the InterPro site	Hours	Inconsistent	Manual	Constant
Writing your own API client	Days	Depends	Manual	You own the upkeep

🚀 How to use

1. Create a free Apify account using this sign-up link.
2. Open the InterPro Protein Families Scraper.
3. Either paste a list of accessions, or leave it empty and pick a type to browse.
4. Set maxItems to the number of records you want.
5. Click Start and grab your results when the run finishes.

💼 Business use cases

Bioinformatics and annotation

Goal	How this helps
Annotate proteins with families	Pull entries with signatures and GO terms
Map domains across a proteome	Browse by type and join on accession

Database and tool building

Goal	How this helps
Seed a local InterPro mirror	Walk the catalog with paging built in
Power a domain lookup service	Feed it accession, name, and signatures

Research and analysis

Goal	How this helps
Study family coverage	Use protein, structure, and taxa counts
Trace related superfamilies	Follow the overlapsWith links

Teaching and reference

Goal	How this helps
Build course datasets	Export a curated set of accessions
Create reference sheets	Use the cleaned descriptions and short names

🔌 Automating InterPro Protein Families Scraper

Connect runs to the tools you already use:

• Make and Zapier to trigger runs and route records into sheets or databases.
• Slack to post a summary when a run finishes.
• Airbyte to load results into a warehouse.
• GitHub Actions to schedule periodic snapshots.
• Google Drive to archive each run's output.

🌟 Beyond business use cases

• Research: study how protein family classifications are organized.
• Personal: build your own domain reference for a favorite protein.
• Non-profit: power an open educational resource on protein biology.
• Experimentation: prototype an annotation tool without writing a scraper.

🤖 Ask an AI assistant

Paste your results into ChatGPT, Claude, Perplexity, or Microsoft Copilot and ask it to summarize a family, group entries by member database, or explain the GO terms attached to a domain.

❓ Frequently Asked Questions

Do I need an InterPro or EBI account? No. The Actor reads the public InterPro REST API, which needs no login.

Do I need an API key? No key is required.

How do I fetch specific entries? Put their accessions in the accessions list, for example IPR000001. When that list is filled, the type filter is ignored.

How do I browse the whole catalog? Leave accessions empty and set maxItems. Optionally pick a type to narrow the browse.

Which entry types are supported? Family, domain, homologous_superfamily, repeat, conserved_site, active_site, binding_site, and ptm, plus an any option.

How many entries are there? At the time of writing, the InterPro API reports more than 51,000 entries.

Are member database signatures included? Yes. Each record lists the contributing databases and an expanded array of signatures with database, accession, and name.

Are GO terms included? Yes, when InterPro has assigned them. Each GO term carries its identifier, name, and category.

Why is the description cleaned up? InterPro descriptions contain HTML and citation markers. The Actor strips those so you get plain readable text.

Can I schedule this? Yes. Use Apify Schedules to snapshot the catalog on any cadence.

🔌 Integrate with any app

Results are available through the Apify API, so you can pull them into any app, database, or workflow you already run.

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💡 Pro Tip: browse the complete ParseForge collection.

🆘 Need Help? Open our contact form

⚠️ Disclaimer: independent tool, not affiliated with InterPro, EMBL-EBI, or the European Bioinformatics Institute. Only publicly available data is collected.