InterPro Protein Families Scraper

InterPro Protein Families Scraper

Scrape InterPro protein family entries by accession or browse by type, up to a million per run. Every entry returns its name, type, accession, source database, and source organism. Export to JSON, CSV, Excel, or XML.

InterPro classifies proteins into families and predicts domains and important sites, but downloading entries one by one through the web interface is slow. This Actor reads the public InterPro entry pages directly, fetching exactly the accessions you list or browsing all entries filtered by type. Each match lands in your dataset as one flat row with a fixed schema.

Who uses it	What they scrape InterPro for
Bioinformaticians	Building a local catalog of protein family signatures for a custom annotation pipeline.
Computational biologists	Gathering domain and site annotations across a target set of InterPro accessions for comparative genomics.
Data curators	Auditing InterPro entry metadata such as source databases and contributing organisms for quality control.

What it does

This Actor collects InterPro protein family entries by accession list or by browsing a chosen entry type, and returns each entry as a flat row with its name, type, accession, source database, and source organism.

• 🎯 Targeted accession fetch: provide a list of InterPro accessions like IPR000001 and the Actor retrieves exactly those entries, ignoring the type filter.
• 📂 Browse by entry type: leave the accession list empty and pick a type such as Family, Domain, or Binding site to crawl all matching entries.
• 📊 Structured output: every entry comes out as a flat row with name, type, accession, source database, and source organism, ready for analysis.

Results export to CSV, JSON, Excel, or XML, or straight from the API.

What you can do with InterPro data

🧬 Build a protein signature reference set.

A bioinformatician provides a list of InterPro accessions for known domains and the Actor fetches their metadata to seed an internal annotation database.

🔍 Audit InterPro entries by type.

A curator browses all entries classified as 'Conserved site' and exports the source database and organism fields to check annotation consistency.

📋 Collect metadata for comparative genomics.

A computational biologist pulls every 'Family' entry and uses the source organism field to map which taxa contribute to each protein family.

Why choose this scraper

	What you get
Targeted or broad	Fetch specific accessions you care about, or browse every entry of a chosen type.
Fixed schema	Every row shares the same fields: name, type, accession, source database, and source organism.
No API key	Reads the public InterPro pages directly with no registration or authentication.

How it compares

This Actor and the alternative InterPro scraper both collect InterPro entry metadata. The table below highlights the capabilities each listing describes.

Feature	ParseForge	Interpro Protein Families Scraper
Fetch by accession list	Yes	Not listed
Browse by entry type	Yes	Not listed
Source organism field	Yes	Not listed
Export to JSON, CSV, Excel, XML	Yes	Yes
Up to 1 million entries per run	Yes	Not listed

Configure the run

Drive the Actor from a list of InterPro accessions or by browsing a single entry type, and set a maximum number of entries so your dataset stays within the size you need. The Input tab lists every parameter.

A first run with the defaults:

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

A larger pull:

{
  "accessions": [
    "IPR000001",
    "IPR000003",
    "IPR000006"
  ],
  "maxItems": 200
}

Pricing

Pay-per-result: $0.017 per result collected. You pay only for the results written to your dataset.

Results collected	Approximate cost
100 results	$1.70
1,000 results	$17.00
10,000 results	$170.00

New Apify accounts start with $5 in free credit.

Free users

Free-plan runs return up to 10 results as a preview. Upgrade your Apify plan to collect up to 1,000,000 results per run.

Run it

1. Create a free Apify account with $5 in credit.
2. Open the InterPro Protein Families Scraper.
3. Set your inputs and any filters, then click Start.
4. Export the results as CSV, Excel, JSON, or XML from the Dataset tab.

Run it programmatically through the Apify API (run-sync-get-dataset-items) or the ApifyClient for JavaScript and Python.

Use with AI agents (MCP)

Give an AI agent live access to InterPro through the Model Context Protocol. Add the Actor to Claude, Cursor, or any MCP client:

$claude mcp add --transport http apify "https://mcp.apify.com?tools=parseforge/interpro-protein-families-scraper"

Then prompt it in plain language to run the scraper and read back the results.

Troubleshooting

Why am I getting no results?

Check that your accessions are valid InterPro identifiers like IPR000001. If you left the accessions list empty, make sure you selected an entry type other than 'Any type' and that the maximum entries is set to a number greater than zero.

The run is taking too long.

Lower the maximum entries value to reduce the number of pages the Actor visits. If you are browsing by type, pick a narrower type to limit the crawl scope.

Some accessions I listed are missing from the output.

Verify that the accession string is spelled correctly and that the entry still exists on the InterPro website. The Actor skips accessions that return a page not found error.

The output contains fewer rows than my maximum entries setting.

The Actor stops when it has collected the requested number of entries or when no more entries of the chosen type are available. Try a broader type or a higher limit if you need more data.

FAQ

Question	Answer
Can I fetch a specific list of InterPro accessions?	Yes. Fill the accessions list with entries like IPR000001 and the Actor will retrieve exactly those entries, ignoring the type filter.
How do I browse all entries of one type?	Leave the accessions list empty and choose an entry type from the dropdown, such as Family or Domain. The Actor will crawl all matching entries up to your maximum limit.
What fields does each row contain?	Every row includes the entry name, type, accession, source database, and source organism. The exact field list is shown in the sample output on the Actor's page.
Is there a rate limit or do I need an API key?	No API key is required. The Actor reads the public InterPro entry pages. You can control the volume with the maximum entries setting.
Can I export the results to CSV or Excel?	Yes. The dataset can be exported in JSON, CSV, Excel, or XML formats directly from your Apify run.
What happens if I provide both accessions and an entry type?	When the accessions list is not empty the type filter is ignored. The Actor fetches exactly the accessions you listed.
How many entries can I collect in one run?	You can set the maximum up to one million entries per run. The default is 10 for quick tests.
Does this Actor handle PTM and binding site entries?	Yes. The entry type filter includes PTM, binding site, active site, and conserved site, alongside families, domains, repeats, and homologous superfamilies.

Related actors

Browse the full ParseForge collection for more scrapers.

🆘 Need help? Email parseforge@protonmail.com with your run ID, your input, and what you expected.

⚠️ Disclaimer. This Actor is unofficial and is not affiliated with, endorsed by, or sponsored by EMBL-EBI. It collects only publicly available data. You are responsible for using the collected data in compliance with the source's terms of service and applicable data-protection laws, including GDPR, CCPA, and PIPL. Do not use it to collect personal data unlawfully.