Protein Data Bank in Europe (PDBe)

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#AlphaFold #Bioinformatics #StructuralBiology

AlphaFold Database welcomes community datasets Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities

The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities.

This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.

Explore the new datasets in the AlphaFold Database.

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

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...

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...

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

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

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

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

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

Latest time-stamped copies of the PDB and EMDB archives are now available.

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

This is just the beginning. Planned developments include clustering of conformational states and a new interface tab to support deeper analysis of macromolecular interactions.

🔗 Explore the SARS CoV 2 spike complex via PDB entry 9CXE
www.ebi.ac.uk/pdbe/pdbe-kb...

PDBe-KB Complexes aggregates equivalent assemblies from across the PDB into unified complex level records. This enables systematic comparison of composition, stoichiometry, symmetry, ligands, and assembly properties across experiments and conditions.

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…

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

The wreath was created using PDB entry 8PDN, with the red bow from EMD-35864. Snowflakes were created using PDB entries 6MQA, 7NI2, 8KG2 and EMDB maps EMD-9861, EMD-15602, EMD-23388, EMD-30158, EMD-32016, EMD-35178, EMD-44639, EMD-50640. Yellow stars were created using PDB entries 6HIF and 8OZL.

🎄✨ 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.

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...

🆕 New to the pages?
Try the interactive tour or the PDBeChem training module:
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💬 Share your feedback:
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Looking for ligand–protein interactions?
See which proteins a ligand binds, the key amino acids involved, and the functional role of the ligand—directly on the page.

🔬 What can you find on the Ligand pages?
• Standardised identifiers
• Physicochemical properties
• Bound structures
• Protein interactions
• Similar ligands and stereoisomers
• External resource links

🚀 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

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.