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
By 2028, all 4-character PDB IDs will be exhausted.

After that, all new entries will receive extended IDs: 12 characters total, formatted as pdb_ + 8 alphanumeric characters (pdb_1000axyz)

Test it from PDB Beta Archive

Read more: www.wwpdb.org/news/news?ye...
February 12, 2026 at 11:32 AM
We’re running a survey to learn your experience with AlphaFold DB search results and filters.

Take 5-minutes to share your experience with AlphaFold DB search and have a say in upcoming improvements.

Fill in the survey forms.gle/K7RotPrD9ZPZ...

#AlphaFold #Bioinformatics #StructuralBiology
Search survey
This survey asks about how you browse and choose results in AlphaFold DB search. We are interested in which information you rely on, how you use filters, and how you interpret key attributes when deci...
forms.gle
February 11, 2026 at 11:24 AM
We're hiring a 𝐓𝐫𝐚𝐢𝐧𝐢𝐧𝐠 𝐒𝐩𝐞𝐜𝐢𝐚𝐥𝐢𝐬𝐭 for 𝐀𝐥𝐩𝐡𝐚𝐅𝐨𝐥𝐝 𝐃𝐚𝐭𝐚𝐛𝐚𝐬𝐞 (AFDB)! Join our team to develop training content, create workshops, and drive global engagement with AlphaFold and AFDB.

Full-time, hybrid role.

Apply now! embl.wd103.myworkdayjobs.com/en-US/EMBL/d...

#AFDB #Jobs #emblebi
January 26, 2026 at 10:55 AM
The wwPDB just hit a major milestone: 𝟏𝟎,𝟎𝟎𝟎 𝐄𝐌𝐃𝐁 𝐞𝐧𝐭𝐫𝐢𝐞𝐬 𝐫𝐞𝐥𝐞𝐚𝐬𝐞𝐝 𝐢𝐧 𝐚 𝐬𝐢𝐧𝐠𝐥𝐞 𝐲𝐞𝐚𝐫. To put this in context, the entire EMDB reached 10,000 entries total in 2019 — now the archive 𝐡𝐚𝐬 𝐬𝐮𝐫𝐩𝐚𝐬𝐬𝐞𝐝 𝟓𝟎,𝟎𝟎𝟎. Huge credit to the community driving 3DEM forward!

www.wwpdb.org/news/news?ye...

#3DEM #EMDB
EMDB Surpasses 10,000 Entries in a Year
wwPDB: Worldwide Protein Data Bank
www.wwpdb.org
January 20, 2026 at 10:18 AM
Find out how to answer scientific questions about #ligands in the #PDB directly from your web browser. Watch the latest talk by Ibrahim Roshan at the CCP4 Study Weekend 2026.

🎥 Watch the talk:
ukri.zoom.us/rec/play/U_J...

#PDBeKB #CCP4 #StructuralBiology
January 14, 2026 at 10:46 AM
Join us at the IUCr 2026 Congress
📍 Calgary, Alberta (Canada)
📅 August 11–18, 2026

👉 Register now and sign up for a free half-day, hands-on wwPDB workshop:
event.fourwaves.com/iucr-2026/re...

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

#IUCr2026 #Crystallography #wwPDB
Event Website - Fourwaves
Event Website
event.fourwaves.com
January 12, 2026 at 10:39 AM
Latest time-stamped copies of the PDB and EMDB archives are now available.

Read more: www.wwpdb.org/news/news?ye...
Time-stamped Copies of PDB and EMDB Archives
wwPDB: Worldwide Protein Data Bank
www.wwpdb.org
January 8, 2026 at 12:18 PM
PDBe-KB Complexes has been published in
@jmolbiol.bsky.social at the start of the new year, introducing a complex centric view of experimentally determined macromolecular assemblies in the PDB.

📄 Read the paper: sciencedirect.com/science/arti...

#PDBeKB #MacromolecularComplex #Bioinformatics
PDBe-KB Complexes: Enabling Functional Insight from Macromolecular Complexes in the PDB
PDBe-KB Complexes is a set of webpages that aggregate experimentally determined macromolecular assemblies into unique complex-level records within the…
sciencedirect.com
January 5, 2026 at 2:04 PM
🎄✨ Season’s Greetings from PDBe ✨🎄
The PDBe wishes you a very Merry Christmas and a Happy New Year. We are delighted to share our jointly designed EMDB/PDBe Christmas card with you. It has been a busy year, and we look forward to seeing you in the New Year.
December 18, 2025 at 2:12 PM
Milestone reached: Over 20,000 new structures deposited to the PDB in 2025!

This reflects advances in cryo-EM, high-throughput crystallography, and AI-driven modelling, supported by expert wwPDB biocuration and open data sharing.

Read more: wwpdb.org/news/news?ye...
December 17, 2025 at 4:14 PM
🚀 Update Alert
The new PDBe-KB Ligand pages are live with a cleaner layout, intuitive tabs, and a brand-new onboarding tour to help you get started.
Explore here 👉 pdbe.org/chem/STI
December 10, 2025 at 3:44 PM
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-...
December 4, 2025 at 2:00 PM
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...
December 2, 2025 at 1:30 PM
🌍 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
November 20, 2025 at 12:00 PM
🚀 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
Reposted by Protein Data Bank in Europe (PDBe)
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!
AlphaFold Protein Structure Database
AlphaFold Protein Structure Database
alphafold.com
October 22, 2025 at 5:40 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
Reposted by Protein Data Bank in Europe (PDBe)
Registrations are open for the MDDB conference!

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

#MDDB #OpenScience #FAIRdata
📣 Mark your calendars for the MDDB Conference!

📅 February 3-5, 2026
📍 Lausanne, Switzerland

Join us for an inspiring event with outstanding speakers and experts in the field!

Read more and register here ➡️ mddbr.eu/conference/

#MDDB #OpenScience #FAIRdata
October 13, 2025 at 1:04 PM
Reposted by Protein Data Bank in Europe (PDBe)
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
October 7, 2025 at 2:03 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
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
September 24, 2025 at 9:08 AM
Reposted by Protein Data Bank in Europe (PDBe)
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
🧬🖥️
September 23, 2025 at 10:38 AM
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
September 19, 2025 at 9:30 AM