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Reposted by Protein Data Bank in Europe (PDBe)

EMBL-EBI @ebi.embl.org · 1d

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

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 1d

📣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...

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 14d

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...

wwPDB: 2025 News

wwPDB: Worldwide Protein Data Bank

www.wwpdb.org

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Reposted by Protein Data Bank in Europe (PDBe)

EMBL-EBI @ebi.embl.org · 15d

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
🧬🖥️

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 19d

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...

New PDBe entry pages: Interactive, personalised, and mobile-ready

Explore molecular structures with new interactive 3D viewers and AI annotations

www.ebi.ac.uk

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 27d

🧪 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

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 29d

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

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Sep 5

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

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Sep 5

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

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Sep 4

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

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Sep 4

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

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Sep 4

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

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Sep 4

🚀 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

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Aug 29

🚨 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...

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Aug 27

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

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Aug 27

🔬 PDBe is excited to be at #ECM35, in Poznan, Poland 🤍❤️, joint hosted by Lviv, Ukraine 💙💛!

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

Crystallography continues to unlock the secrets of biomolecular structures!

#Biology # Chemistry

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Reposted by Protein Data Bank in Europe (PDBe)

CATH-Gene3D @cathgene3d.bsky.social · Aug 22

CATH turns 30 years old this year!

We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses.

www.eventbrite.co.uk/e/protein-an...

Protein Annotations in the age of AI

A not-for-profit symposium hosted at UCL - more details about speakers and venue below.

www.eventbrite.co.uk

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Aug 21

Every annotation is traceable to its publication 📄. Open the PubMed link and delve even deeper. Download annotations through our API.

Try yourself: wwwdev.ebi.ac.uk/pdbe/entry/p...

#PDBeBeta #OpenScience #ProteinData #AnnotationsAPI #ARISE #IUCr

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Aug 20

🚀 Since Spring 2024, these metrics are available via emdatabank.org. wwPDB is adding Q score sliders to validation reports.

👉 Paper: lnkd.in/ejE6j4yS
👉 Announcement: lnkd.in/eHa8j947

#StructuralBiology #Validation #Qscore

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Aug 20

📄 New paper: 3DEM Structure Map Validation Recommendations

Two new metrics assess model-to-map fitness in cryo-EM:
🔹 Q_relative_all → compares avg Q-score across PDB/EMDB
🔹 Q_relative_resolution → compares within similar resolution

#3DEM #CryoEM #wwPDB

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Aug 15

Explore 🧭 a residue’s structural environment in the context of its linked annotations. Colour-coding 🖍️ residues in the sequence points you to places of interest, go and discover.

Try yourself: wwwdev.ebi.ac.uk/pdbe/entry/p...

#PDBeBeta #ResidueLevelInsights #PDBeValidation #ARISE #IUCr

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Aug 14

We’ve listened!
Thanks to your feedback on last week’s AlphaFold DB redesign, we have
✅ Added interactive sequence navigation
✅ Made downloads faster clearer
✅ Listed the PDB coordinate file as its own option
Keep the feedback coming
🔗 alphafold.ebi.ac.uk/entry/P09958

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Aug 13

The page is back up now ✅ Thanks again for letting us know!

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Aug 13

Appreciate the heads-up! We’re checking it out and will get it fixed soon.

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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Aug 13

Click on a residue in the sequence viewer or 3D Mol* viewer and watch everything sync! 🎯 Just like magic ✨ — all while zooming in on the structure in real-time.

Try yourself: wwwdev.ebi.ac.uk/pdbe/entry/p...

#PDBeBeta #Molstar #Bioinformatics #ResidueLevelInsights #ARISE #IUCr

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