RCSB PDB Protein Structure Scraper

RCSB PDB Protein Structure Scraper

Scrape protein structure metadata from RCSB PDB by keyword, experimental method, or explicit PDB ID, up to a million entries per run. Each structure row includes resolution, release date, authors, and entity counts. No API key required. Export to CSV, JSON, Excel, or XML.

The RCSB PDB search API returns paginated JSON, but you still need to handle cursor logic, rate limits, and schema mapping yourself. This Actor reads the public search and entry endpoints directly, filters by experimental method like cryo-EM or X-ray diffraction, and returns every matching structure in one flat, predictable schema.\n\nIt works for one-off lookups by PDB ID and for bulk keyword searches across the entire archive.

Who uses it	What they scrape RCSB PDB for
Structural biologists	Pull a clean dataset of all cryo-EM structures for a protein family to compare resolution trends.
Bioinformatics engineers	Feed a pipeline with fresh PDB entries matching a gene name, enriched with entity counts and deposition dates.
Cheminformatics researchers	Gather ligand-bound structures by keyword and experimental method for docking studies.
Science data journalists	Track how many SARS-CoV-2 structures were released each month by method.

What it does

This Actor collects RCSB PDB protein structure metadata by keyword search or explicit PDB ID list and returns each structure as a flat row with resolution, method, authors, and release dates.

• 🔬 Experimental method filter: restrict results to X-ray diffraction, cryo-EM, solution NMR, neutron diffraction, and more.
• 🆔 PDB ID mode: pass a list of 4-character PDB IDs to fetch exact entries, bypassing search entirely.
• 🔍 Full-text search: query by protein name, gene, organism, or ligand and get back every matching structure.
• 📦 Bulk collection: set a high maxItems to pull thousands of structures in one run for archive-scale analysis.

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

What you can do with RCSB PDB data

📊 Compare resolution by method.

A structural biologist pulls all hemoglobin structures, filters by X-ray diffraction and cryo-EM, and plots resolution distributions to justify a method choice for a new study.

🧬 Feed a protein annotation pipeline.

A bioinformatics engineer runs a weekly keyword search for a gene name, collects new PDB entries, and pushes the metadata into an internal annotation database.

💊 Gather ligand-bound structures for docking.

A cheminformatician searches for a drug target keyword, restricts to X-ray structures, and exports a CSV of PDB IDs with ligand entity counts for virtual screening.

📈 Monitor structure release trends.

A data journalist runs monthly searches for a disease keyword, groups results by deposition date, and reports on structural biology output over time.

Why choose this scraper

	What you get
No API key or registration	The Actor reads the public RCSB PDB endpoints, so you skip app registration and authentication.
Fixed flat schema	Every run returns the same columns: title, method, resolution, authors, dates, and entity counts.
Method-aware filtering	Filter by nine structure determination methods, from X-ray diffraction to solution scattering.
PDB ID precision	Fetch exact entries by their 4-character PDB ID when you already know which structures you need.

How it compares

This Actor focuses on fast, filterable metadata collection from RCSB PDB alone, while the competitors below either add cross-database resolution or monitor release changes.

Feature	ParseForge	RCSB PDB Structures Scraper	Protein Structure Evidence Resolver	Protein Structure Release Monitor
Keyword search across RCSB PDB	Yes	Yes	Not listed	Not listed
Filter by experimental method	Yes, nine methods including cryo-EM and NMR	Not listed	Not listed	Not listed
Fetch by explicit PDB ID list	Yes	Not listed	Not listed	Not listed
Cross-database evidence resolution	Not listed	Not listed	Yes, across RCSB PDB, PDBe, AlphaFold DB, and UniProt	Not listed
Release monitoring with diffs	Not listed	Not listed	Not listed	Yes, monitors releases and revisions with baselines
No API key required	Yes	Not listed	Not listed	Not listed

Configure the run

Drive the Actor from a keyword search or a list of PDB IDs, and narrow results by experimental method so only relevant structures land in your dataset. The Input tab lists every parameter.

A first run with the defaults:

{
  "searchQuery": "hemoglobin",
  "pdbIds": [],
  "maxItems": 10
}

A larger pull:

{
  "searchQuery": "hemoglobin",
  "pdbIds": [],
  "maxItems": 200
}

Pricing

Pay-per-result: $0.0385 per result collected. You pay only for the results written to your dataset.

Results collected	Approximate cost
100 results	$3.85
1,000 results	$38.50
10,000 results	$385.00

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 RCSB PDB Protein Structure 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 RCSB PDB 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/rcsb-pdb-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 searchQuery is spelled correctly and is not too specific. Try a broader term like a protein family name. If you are using pdbIds, verify each ID is a valid 4-character PDB entry. Also confirm the experimentalMethod filter is not excluding all matches.

Why does my run time out?

Large maxItems values combined with broad searches can take time because the Actor pages through results politely. Increase the run timeout in the Apify console, or reduce maxItems to a smaller batch.

Why are some fields empty in my output?

Not every PDB entry has every field populated. For example, some older structures may lack a resolution value, and NMR structures often do not report resolution the same way X-ray structures do. Empty cells reflect missing data at the source.

Why did my pdbIds input get ignored?

The pdbIds field overrides searchQuery only when it contains at least one valid 4-character ID. If the list is empty or the IDs are malformed, the Actor falls back to the searchQuery. Double-check the format and try again.

Why am I getting fewer results than maxItems?

The Actor stops when the RCSB PDB search API returns no more matching structures. If your search query or method filter matches fewer structures than your maxItems value, you will get all of them and the run will finish early.

FAQ

Question	Answer
Do I need an API key or RCSB PDB account?	No. The Actor reads the public RCSB PDB search and entry endpoints directly. No registration, API key, or authentication is required.
What data fields does each row include?	Each row returns the PDB ID, title, experimental method, resolution, release date, deposition date, author list, entity counts, and the canonical structure URL. The exact field list is shown in the sample output on the Actor's page.
Can I fetch specific PDB IDs instead of searching?	Yes. Pass a list of 4-character PDB IDs in the pdbIds input field, and the Actor will fetch those exact entries, ignoring any search query.
How do I filter by experimental method?	Use the experimentalMethod dropdown in the input. You can select X-ray diffraction, cryo-EM, solution NMR, neutron diffraction, solid-state NMR, electron crystallography, fiber diffraction, powder diffraction, or solution scattering.
What happens if my search returns thousands of structures?	Set the maxItems field to control how many structures the Actor collects. The RCSB PDB search API returns results in pages, and the Actor handles pagination automatically up to your limit.
Can I search by gene name or organism?	Yes. The searchQuery field performs a full-text search across the RCSB PDB archive, which indexes protein names, gene names, organisms, ligands, and authors.
Does this Actor download PDB coordinate files?	No. This Actor collects metadata only: titles, methods, resolution, dates, authors, and entity counts. For coordinate file downloads, you would need a different tool.
How often is the RCSB PDB data updated?	The RCSB PDB releases new and revised structures every week. The Actor queries the live search API, so you always get the current archive contents.
Can I export the results to CSV?	Yes. Like all Apify Actors, you can export your dataset to CSV, JSON, Excel, or XML directly from the run console.
Is there a rate limit?	The Actor respects the RCSB PDB public API rate limits and includes polite delays between requests. For very large runs, it may take longer but will complete without being blocked.

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 RCSB Protein Data Bank. 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.