Protein Data Bank in Europe (PDBe)

The latest update to the AlphaFold Database (AFDB) is now published in NAR.

The release aligns AFDB with UniProt 2025_03 and introduces a redesigned entry page with integrated annotations, domains, summaries, and a 3D viewer.

📄 Read more: academic.oup.com/nar/advance-...

We’re still improving — thanks to you!
Our latest PDBe entry page update adds smoother browsing, better 3D selections, and direct links to page sections.

Examples:
Macromolecule:
www.ebi.ac.uk/pdbe/entry/p...

Ligand:
www.ebi.ac.uk/pdbe/entry/p...

Complex:
www.ebi.ac.uk/pdbe/entry/p...

🌍 Coming soon: wwPDB deposition workflow update

Starting Jan 2026, data depositions will be redistributed:
• PDBj → Oceania + most of Asia (except China)
• PDBc → China
• RCSB PDB → Americas
• PDBe → Europe & Africa

🚀 Introducing PDBe-KB Complexes — a new PDBe-KB resource for exploring macromolecular complexes across the PDB.

🔗 Explore (SARS-CoV-2 spike, PDB 9CXE): ebi.ac.uk/pdbe/pdbe-kb...

📄 Read the preprint: ssrn.com/abstract=568...

#PDBeKB #MacromolecularComplexes #StructuralBiology

PDBe adopts the new DSSP for protein secondary structure annotation | Protein Data Bank in Europe Advanced Search

The new DSSP version 4 uses mmCIF as its primary format and extends secondary structure detection to include left-handed polyproline II (κ) helices, common motifs that contribute to protein folding and stability.

Full announcement: www.ebi.ac.uk/pdbe/news/pd...

#PDBe #DSSP #ProteinStructure

PDBe has adopted the latest DSSP (Define Secondary Structure of Proteins), developed by the PDB-REDO team at the Netherlands Cancer Institute, as its standard tool for annotating protein secondary structure across all PDB entries.

wwPDB: Worldwide Protein Data Bank wwPDB: Worldwide Protein Data Bank

The effort adopts community tools like FindGeo (MetalPDB) and MetalCoord (CCP4).
Details and example files are available at wwPDB.org
.
For queries: info@wwpdb.org

This update will affect ~900 metal-containing CCDs and ~13,000 PDB entries, with public release planned for Q3 2026.
It includes improved charge standardisation, metal coordination and π-bond annotation, and geometry information.

Metalloproteins make up ~30% of the PDB archive.
To ensure FAIR data practices, wwPDB is remediating existing polyatomic metal-containing entries and CCDs — improving their chemical and coordination descriptions for better findability and reuse.

Your direct links to structures have a new format.

Old: alphafold.com/entry/P40763
New: alphafold.com/entry/AF-P40...

Simply add 'AF-' and '-F1' to the UniProt ID. Update your bookmarks and code!

MSAs are listed on each entry page on the top right-hand side in a drop-down list. Bulk access is not currently available.

Want exact accessions per category?
FTP: ftp.ebi.ac.uk/pub/database...
Files: “diffs.ndjson.gz” (per-release diff), “accession_ids.csv” (current v6 set).
See “README.txt” there for field definitions.

“Added/Removed” track UniProt additions/archives, and 40,054 isoforms added
“Changed” = sequence changed (not metadata).
“Unchanged” = metadata updated to current UniProt; entries relabelled v6.

AlphaFold DB v6 (synced with UniProt 2025_03) is live! Here are the details:
Totals v4 → v6: 241,070,489 entries.
Since v4: +65,711,653 added, 39,324,993 removed, 276,539 changed (in sequence), 175,082,297 unchanged (metadata refresh, relabelled v6). Details 👇

Registrations are open for the MDDB conference!

Find out more, register, submit your abstract ➡️ mddbr.eu/conference/

#MDDB #OpenScience #FAIRdata

We’re renewing our collaboration with Google DeepMind!

We'll keep developing the AlphaFold Database to support protein science worldwide 🎉

To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.

www.ebi.ac.uk/about/news/t...

🖥️🧬 #AlphaFold
@pdbeurope.bsky.social

📣Important update for #AlphaFold API users! New API fields launched on October 7th, 2025. We’ll maintain BOTH fields until June 25, 2026! Check the docs! 🔗
For more information, read the news item: www.ebi.ac.uk/pdbe/news/br...

wwPDB: 2025 News wwPDB: Worldwide Protein Data Bank

Introducing the first 3DEM Model-Map percentile slider to the wwPDB validation report

From Oct 1, all new 3DEM entries will include the Q-score percentile slider — helping users quickly assess model–map fit quality across EMDB/PDB archives.

Read more: www.wwpdb.org/news/news?ye...

Do you study proteins?
The new PDBe entry pages make it easier to explore protein structures.

🟢 Visualise ligands & macromolecules with improved 3D viewers
🟢 Get background info from AI-based annotations
🟢 Add your own annotations to viewers without leaving the browser

@pdbeurope.bsky.social
🧬🖥️

New PDBe entry pages: Interactive, personalised, and mobile-ready Explore molecular structures with new interactive 3D viewers and AI annotations

Making structural biology data accessible to everyone — from specialists to first-time explorers.

✨ Discover the new interactive, personalised & mobile-ready PDBe Entry Pages.
📖 Read more: www.ebi.ac.uk/about/news/u...

🔍 Try it: www.ebi.ac.uk/pdbe/entry/p...

🧪 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: tinyurl.com/pdbekb-compl...

#PDBeKB #Complexes #Bioinformatics #StructuralBiology #Science

What can you do with PDBe-KB Complexes (beta)?
🗂️ Unified view of PDB assemblies
🧬 Standardised annotations
📊 Structural metrics and interactive visualisations
🔗 wwwdev.ebi.ac.uk/pdbe/pdbe-kb...
#PDBeKB #Complexes #Bioinformatics #StructuralBiology #Science

💬 Your responses will help guide future improvements to the tool.
🙏 Thank you for helping us make PDBePISA more useful for the community!

🔬 Structural biologists, help us improve the PDBePISA server!
Fill in a 6-minute survey about your experience with PDBePISA
forms.gle/PfoCYHJe1y9L...

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

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

🔗 Open the complex page from a PDB ID
Auto-resolves to the entry’s preferred assembly.
Format: ../complexes/{pdb_id}
Example: ../complexes/1a00

🚀 PDBe-KB Complexes (beta) is now live!
Same macromolecular complex. Different experimental conditions. All assemblies in one place.

🔍 Try the beta now: wwwdev.ebi.ac.uk/pdbe/pdbe-kb...

#PDBeKB #Complexes #Bioinformatics #StructuralBiology #Science

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

PDBe brings new updated REST API endpoints that fully replicates the functionality of the old service, while introducing performance enhancements and additional endpoints.

⬇️ Read more⬇️

www.ebi.ac.uk/pdbe/news/un...

A poster from the PDBe team viewable Thursday & Friday at #ECM35

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

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

#Biology #Chemistry