Protein Data Bank in Europe (PDBe)
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pdbeurope.bsky.social
Protein Data Bank in Europe (PDBe)
@pdbeurope.bsky.social
Developing macromolecular structure resources and tools for life science.
- Founding partner of the wwPDB.
- Manage the community-led PDBe-KB resource and the AlphaFold Protein Structure Database, a collaboration with Google DeepMind.
- Part of EMBL-EBI
🚀 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
November 12, 2025 at 3:16 PM
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.
October 30, 2025 at 4:22 PM
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.
October 28, 2025 at 2:43 PM
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 👇
October 21, 2025 at 1:00 PM
📣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...
October 7, 2025 at 2:49 PM
🧪 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
September 11, 2025 at 2:22 PM
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
September 9, 2025 at 1:50 PM
🔬 Structural biologists, help us improve the PDBePISA server!
Fill in a 6-minute survey about your experience with PDBePISA
forms.gle/PfoCYHJe1y9L...
September 5, 2025 at 1:02 PM
🚀 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
September 4, 2025 at 1:29 PM
🚨 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...
August 29, 2025 at 1:45 PM
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
August 27, 2025 at 6:00 PM
🔬 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
August 27, 2025 at 9:00 AM
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
August 21, 2025 at 12:59 PM
📄 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
August 20, 2025 at 12:53 PM
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
August 15, 2025 at 12:47 PM
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
August 14, 2025 at 1:07 PM
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
August 13, 2025 at 1:05 PM
🧬 🔨 Residue-level insights powered by AI. Explore insight for specific amino acids from primary literature #TextMining

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

🔗 wwwdev.ebi.ac.uk/pdbe/entry/p...

#AIinBiology #Biology #Science #ARISE #IUCr
August 12, 2025 at 4:41 PM
This artwork, inspired by a Chinese cobra 🐍 venom protein, uses red and green to depict danger and healing.

Cardiotoxins ☠️ in #snake venom target the heart ❤️.

Article on the science-behind-the-art ⬇️
www.ebi.ac.uk/pdbe/article...

#SciArt #PDBart #Poison #NatureArt
August 1, 2025 at 1:05 PM
📢 New online on-demand course:
👉 www.ebi.ac.uk/training/onl...

Not all 3D macromolecular models are created equal!

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

#Biology #Chemistry #Science
August 1, 2025 at 8:45 AM
We were thrilled to represent PDBe (PDBe.org) at #ISMBECCB2025.

A great opportunity to connect with users, collaborators & fellow data enthusiasts alongside our @ebi.embl.org colleagues!

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

#Science #Chemistry #Biology
July 25, 2025 at 10:23 AM
🚀 Macromolecule structures have been front & center at #ISMBECCB2025 in Liverpool -- the world’s largest #bioinformatics meeting!

🗝️ Keynotes:
www.iscb.org/ismbeccb2025...

🧬More strucurtal bionformatics / computational biology talks, #3DSIG stream:
www.iscb.org/ismbeccb2025...

@3dsig.bsky.social
July 24, 2025 at 11:34 AM
PDBe team's posters viewable today at #ISMBECCB2025:
🧪 106 - Shape retrieval methods for the classification of protein surfaces!

Poster abstracts (search by title or name) available here:
www.iscb.org/ismbeccb2025...
July 24, 2025 at 9:45 AM
PDBe team's posters viewable today at #ISMBECCB2025:
🧪 027 - Small molecules in the PDB
🧪 045 - AlphaFold Protein Structure Database
🧪 046 - Fragment-based screening data in the PDB
🧪 247 - Improved PDBe & PDBe-KB webpages

Full titles in images.

Abstracts:
🔗 www.iscb.org/ismbeccb2025...
July 22, 2025 at 2:23 PM
Did you know? The Citations tab shows:
📄 Papers and Reviews citing the structure publication
🔎 Papers and Reviews mentioning the PDB ID
🧬 Figures from open access publications
via our integration with @europepmc.org

#PDBeBeta #Bioinformatics #Bioinformatics #Biochemistry
July 22, 2025 at 12:55 PM