Welcome!
PDBe provides multiple ways to access information from the PDB programmatically. You can retrieve details about samples, experiments, models, compounds, cross-references, publications, quality, assemblies, and more.
There are two main parts of our programmatic access offerings at PDBe
Solr-based query system
The Solr-based query system is a powerful option for searching data in the PDB, offering advanced search options across more than 200 fields.
View the documentation at this URL: www.ebi.ac.uk/pdbe/api/doc/search.html
PDBe REST API
The REST API provides access to both detailed data on individual entries, based on PDB or ligand IDs, and aggregated data across multiple PDB entries, such as by entity, UniProt ID, residue, and more, offering a comprehensive view through a single interface
View the documentation at this URL: www.ebi.ac.uk/pdbe/api/v2/doc
Find out more
For more information, visit the following links:
- Frequently asked questions (FAQ)
- Webinars and materials to learn more about PDBe programmatic access
- PDBe API user mailing list
Why?
3D biomacromolecular structures are crucial for high-impact scientific endeavours, including basic science, disease research, drug discovery, material design, and more. The Protein Data Bank is a substantial resource of macromolecular structure and continues to expand its holdings thanks to experimental advances.
Easy access to structural data is crucial for integrative analyses. The REST API simplifies large-scale data analysis, eliminating the need for bulk file downloads.
We use the API for the PDB and PDBe-KB entry pages
Since the REST API powers our entry pages, they are subjected to a weekly battery of tests. The data sources underlying the REST API are updated weekly, ensuring that the delivered content remains up-to-date.
Who else uses the REST API
Many software packages integrate PDBe REST API calls for quality metrics, cross-references, and visualization. It is widely used by academia and industry groups to support research efforts.
Outlook
The needs of PDBe services and user feedback largely shape the current set of REST API calls. New calls and features are added based on community input. The REST API is envisioned as a long-term, stable, and well-tested resource.
FAQs
How do I subscribe to the mailing list?
Send e-mail to pdbe-api-users-join@ebi.ac.uk. This is a useful channel for us to communicate actively with you about new features, changes, planned downtime, etc.
Where can I find calls and their documentation?
For the PDBe REST API, you can find it at this URL: www.ebi.ac.uk/pdbe/api/doc
Can I request a new call?
Yes — first check if an existing call fits your needs. If not, email the PDBe API user mailing list with details.
How do you test the API?
Many PDBe services use the live API. Bugs and downtime are quickly noticed and fixed. A weekly test suite checks correctness and stability.
How do I report a bug?
Subscribe to the mailing list and report details (OS, language, libraries, call URL, response, status code, etc.). Errors in documentation are also welcome.
How many API calls am I allowed?
Currently, there are no hard limits. Rate limiting may be introduced in future.
How many ids may I include in a POST request?
You can ask for as many as 1000 ids at once.
Why not allow lower-case compound ids?
The Chemical Component Dictionary (CCD) defines IDs in uppercase, and all internal/external sources use uppercase.
Where can I find examples?
How can I stay up to date with new API releases?
Please subscribe to the mailing list. We post information about new calls and updates to existing calls.
Can I make AJAX calls?
Yes — CORS support is enabled on our servers
Can I see an example?
Yes - We have prepared Python examples as Jupyter notebooks that you can use as a template.
