PDBe is a founding member of the wwPDB. The PDBe team is also responsible for the PDBe-KB, AlphaFold DB and 3D Beacons resources.
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Joined October 2010
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🚀 Introducing the NEW PDBe-KB Ligand Search!
🔎 Search by name, ID, formula, SMILES or SMARTs or simply draw a structure to find exact or similar ligands in the PDB.
✨ Multiple ways to search, One intuitive interface!
Try it: pdbe.org/chem
ALT Introducing PDBe-KB Ligand Search. New search interface for ligands in the PDB. New feature.
How do pLDDT, ipTM, ipSAE, pDockQ2 and LIS fit together?
See how these metrics work together to assess confidence in an AlphaFold DB complex interface.
🎬 Watch the full tutorial: youtu.be/k4yBqddtPyQ
#AlphaFold #AlphaFoldDB
Tutorial created by Razan Abbara.
Special thanks to the metrics developers
@RolandDunbrack, @arneelof, @ahramkim1128, together with EBI and GoogleDeepmind members; Sameer Velankar, Jennifer Fleming, @OVKovalevskiy, Melanie Vollmar and Joseph Ellaway.
📢 New in PDBe-KB! Explore MD simulation annotations in ProtVista: residue exposure from MDposit and membrane interactions from MemProtMD.
PDBe and PDBe-KB pages also link to simulations in MDposit.
🔗 ebi.ac.uk/pdbe/pdbe-kb/prote…
ALT PDBe and PDBe-KB now incorporate annotations from molecular dynamics simulations. New feature. MDDB-PDBe integration.
It’s been so exciting to work together on this as part of the @mddbEU project!
A big thank you to our partners: @IRBBarcelona, @BSC_CNS, @UniofOxford, @HelloNostrum, @EPFL_en
A predicted interaction may involve only a small region of a protein complex.
How can we identify confidence in that local interface when surrounding regions have high PAE?
Our tutorial uses PAE matrix to explain how LIS can help 👇
youtu.be/k4yBqddtPyQ
#AlphaFold #AlphaFoldDB
Tutorial created by Razan Abbara.
Special thanks to the metrics developers @RolandDunbrack, @arneelof, @ahramkim1128, together with EBI and GoogleDeepmind members; Sameer Velankar, Jennifer Fleming, @OVKovalevskiy, Melanie Vollmar and Joseph Ellaway.
Protein Data Bank retweeted
Join us for a three-part webinar series on how AI is being used to study proteins, forecast climate risk and simulate new materials.
NVIDIA speakers will be joined by researchers from @emblebi, @OfficialUoM and @EPFL to share how teams are working with NVIDIA BioNeMo, Earth-2 and NVIDIA ALCHEMI.
Sept 23 | Sept 30 | Oct 6
Available in multiple time zones. Register below.
Same predicted complex, different confidence scores:
ipTM: 0.38
ipSAE: 0.75
Why can these metrics differ? Full breakdown 👇
youtu.be/k4yBqddtPyQ
#AlphaFold #AFDB
Tutorial created by Razan Abbara.
Special thanks to the metrics developers @RolandDunbrack, @arneelof, @ahramkim1128, together with EBI and GoogleDeepmind members; Sameer Velankar, Jennifer Fleming, @OVKovalevskiy, Melanie Vollmar and Joseph Ellaway.
🎥 The AlphaFold-Multimer prediction for your protein looks great. But how confident should you actually be in it?
Razan Abbara breaks down the 5 confidence metrics behind every AFDB multimer entry:
pLDDT · ipTM · ipSAE · pDockQ2 · LIS👇
youtu.be/k4yBqddtPyQ
#AlphaFold #AFDB
Special thanks to the metrics developers @RolandDunbrack , @arneelof , & @ahramkim1128 , for their valuable contributions to reviewing this tutorial, together with EBI & GoogleDeepmind members; Sameer Velankar, Jennifer Fleming,@OVKovalevskiy , Melanie Vollmar & Joseph Ellaway.
🚀 New updates improve metalloprotein data across the PDB Archive.
~15,500 PDB entries and ~900 metal-containing CCDs now feature more complete chemical descriptions and metal coordination annotations.
⬇️ More ⬇️
wwpdb.org/news/news?year=202…
#PDB
🚨Get ready for the future of the PDB Archive!
A new publication describes the PDB Beta Archive to support PDB users as they transition to the extended PDB ID and PDBx/mmCIF format. Start preparing for the July 21, 2027 transition.
📄Read here: journals.iucr.org/d/issues/2…
#PDB
🌟Use Shortlinks to Transition to the PDB Beta Archive
Shortlinks make it easier to download data using extended PDB IDs without coding specific file paths.
Start using shortlinks today ahead of the July 21, 2027 transition.
⬇️More ⬇️
wwpdb.org/news/news?year=202…
#PDB
Protein Data Bank retweeted
🤖 Want to use AI and LLMs to unlock molecular dynamics data?
Join #PDBe at #EMBLEBI and help build next-gen MD data integration across PDBe, UniProt, AlphaFoldDB and more.
🌎 Apply from anywhere
🔗 embl.wd103.myworkdayjobs.com…
#AI #StructuralBiology #Database
📄New recommendations for fragment-screening data usage are here.
The white paper summarizes community guidance on the deposition and reuse of structural biology data from fragment screening, hit-to-lead, and lead-optimization studies.
⬇️Read here ⬇️
cdn.rcsb.org/wwpdb/docs/docu…
🚀 Depositors can now submit structures directly to the OneDep system from the structure determination software via a newly developed Deposition API.
Available now in Phenix and CCP-EM Doppio, with CCP4 and Global Phasing support coming soon.
⬇️ more ⬇️
wwpdb.org/news/news?year=202…
Catch mmCIF errors before deposition.
Our new @JApplCryst paper presents the mmCIF Validator: VS Code + Python validation against the official PDBx/mmCIF dictionary.
Paper: doi.org/10.1107/S16005767260…
Code: github.com/PDBeurope/mmcif-v…
#mmCIF #PDB #StructuralBiology
🌟 wwPDB Events at IUCr
Join wwPDB members presenting at the 26th General Assembly and Congress of the International Union of Crystallography (IUCr)
🗓️ August 11-18, 2026
📍 Calgary, Canada
⬇️ More information about presentations here⬇️
🔗wwpdb.org/news/news?year=202…
#PDB