Protein Data Bank in Europe (PDBe)

30/10/2025

11/09/2025

🧪 We're beta testing – and we want your thoughts!

Try the new PDBe-KB Complex pages and let us know:
🔸 What’s working?
🔸 What’s confusing?
🔸 What features are lacking

💬 Feedback form: https://tinyurl.com/pdbekb-complexes-beta-form

09/09/2025

🔍 What can you do with PDBe-KB Complexes (beta)?
Many biological assemblies appear multiple times in the PDB – solved using different methods, under different conditions, and often in distinct functional or conformational states. PDBe-KB Complexes bring these structures together for side-by-side comparison.
📌 Key features
🗂️ Unified view: Explore all PDB assemblies for the same macromolecular complex.
🧬 Standardised annotations: Stoichiometry, symmetry, cofactors, and experimental methods.
💊 Unique bound ligands: Functional types (e.g. drug-like, cofactor-like, reactant-like), with links to assemblies that bind them.
🧩 Complex relationships: Dedicated sections for subcomplexes and supercomplexes.
📊 Structural metrics: Visualisations of PISA-derived assembly properties (e.g. buried surface area, dissociation energy).
🔗 Start exploring:
https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/complexes/1a00

04/09/2025

🚀 We’re excited to launch the beta version of PDBe-KB Complexes, a new addition to the PDBe-KB resource that brings together all experimentally determined structures of the same macromolecular complex.

Many macromolecular complexes are solved multiple times under different experimental conditions, often revealing variations in conformation, ligands, or subunit composition. Until now, these entries were scattered across the archive.

PDBe-KB Complexes provides a unified view where researchers can:
🔬 Explore all PDB assemblies representing the same complex
⚖️ Compare component stoichiometry, ligands, and experimental methods
🧩 Access standardised annotations and interactive visualisations
🌐 Retrieve data via web interface, REST API, and FTP

🔗 Try the beta now:
https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/complexes/1a00

❓ How to open a complex page
Open the complex page from a PDB ID
Auto-resolves to the entry’s preferred assembly
URL format: ../complexes/{pdb_id}
Example: .../complexes/1a00

Open the complex page from a PDBe Complex ID
Jumps straight to that complex
URL format: ../complexes/{pdbe_complex_id}
Example: .../complexes/PDB-CPX-159519

📍 Where to find the PDBe Complex ID:
Each assembly listed on a PDBe entry page includes a PDBe Complex ID

We welcome your feedback as we continue developing this resource!

29/08/2025

*** Unifying PDBe API endpoints- Breaking changes to PDBe API ***

The existing REST API service was built using older technologies, which limited scalability, performance, and ease of maintenance. As demands for better integration and performance have increased, the legacy system no longer meets the standards required for modern application development.

We, therefore, bring a new update to the PDBe API endpoints. This upgrade is part of our broader commitment to continuous improvement—addressing the need for clearer API structure, better documentation, and enhanced responsiveness. By consolidating endpoints and migrating to a newer framework, we’re solving issues around API fragmentation, poor developer experience, and sluggish response times.

What have we done?

Built a new REST API using modern technology that fully replicates the functionality of the old service, while introducing performance enhancements and additional endpoints.

Reorganized and unified API endpoints to improve consistency and usability.

Launched updated Swagger-style documentation at https://lnkd.in/eJCJdtYV, providing developers with a clear and interactive reference.

Established a Deprecation Timeline to help users plan their migration in advance, ensuring a smooth transition.

How does the process/tool work?

The new API follows RESTful principles, offering well-defined, consistent endpoints grouped logically by resource. The new version is built on a high-performance backend framework that reduces latency and improves response times.

How to use it/what is shown?

To start using the new API:
Visit the updated documentation at https://lnkd.in/eJCJdtYV.

Review the updated endpoint paths and any breaking changes.

Begin integrating the new endpoints in your applications.

Use the interactive documentation to test calls and understand expected responses and parameters.

⬇️ Read more⬇️

https://www.ebi.ac.uk/pdbe/news/unifying-pdbe-api-endpoints-breaking-changes-pdbe-api

27/08/2025

A poster from the PDBe team viewable Thursday & Friday at

🧪 MS6_P7 - Building a FAIR Repository for Fragment-Based Screening Campaigns - Presented by Genevieve Evans

All ECM poster titles & abstracts available here:
🔗 https://ecm35.ecanews.org/poster-hiperlinks

27/08/2025

🔬 PDBe is excited to be at , in Poznan, Poland 🤍❤️, joint hosted by Lviv, Ukraine 💙💛!

2026 PDBArt calendars 🎨🗓️ available.
🔗 https://www.ebi.ac.uk/pdbe/pdb-art

Crystallography continues to unlock the secrets of biomolecular structures!

# Chemistry

12/08/2025

🧬 🔨 Residue-level insights powered by AI. Explore insight for specific amino acids from primary literature

🔍 Check out the ⭐ Text Annotations (AI) ⭐ tab on the new pages!

🔗 https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/5cxt?activeTab=llm

07/08/2025

We’ve refreshed the AlphaFold DB entry pages!

Explore the cleaner design, improved 3D viewer, and easier access from any device
➡️ https://alphafold.ebi.ac.uk/entry/P04637

Or read more
➡️ https://ebi.ac.uk/about/news/updates-from-data-resources/new-alphafold-database-entry-pages/

01/08/2025

This artwork, inspired by a Chinese cobra 🐍 venom protein, uses red and green to depict danger and healing.

Cardiotoxins ☠️ in venom target the heart ❤️.

Article on the science-behind-the-art ⬇️
https://www.ebi.ac.uk/pdbe/articles/fangs-death-or-new-bite-life

01/08/2025

📢 New online on-demand course:
https://www.ebi.ac.uk/training/online/courses/analysing-evaluating-macromolecular-models/

Not all 3D macromolecular models are created equal!

Companion to our course, this free tutorial upskills for evaluation of BOTH experimental & predicted models!

25/07/2025

We were thrilled to represent PDBe (PDBe.org) at .

A great opportunity to connect with users, collaborators & fellow data enthusiasts alongside our EBI colleagues!

Thanks to everyone who chatted with us about proteins, RNA, DNA, ligands & more! 🧪✨