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

📢 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. 🔗 www.ebi.ac.uk/pdbe/pdbe-kb...

A predicted interaction may involve only a small region of a protein complex. How can we identify confidence in that local interface when the surrounding regions have high PAE? Our tutorial uses a PAE matrix to explain how LIS can help 👇 youtu.be/k4yBqddtPyQ #AlphaFold #AlphaFoldDB

Same predicted complex, different confidence scores: ipTM: 0.38 ipSAE: 0.75 Why can these metrics differ? Full breakdown 👇 youtu.be/k4yBqddtPyQ #AlphaFold #AFDB

New video 🎥 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

🚀 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 ⬇️ www.wwpdb.org/news/news?ye... #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/202... #PDB

Protein Data Bank (PDB) Archive: a new architecture (beta) for scalable, PDBx/mmCIF-based data distribution

wwPDB has extended PDB IDs to 12 characters with a prefix `pdb_' followed by eight alphanumeric characters in lower case (for example pdb_1000axyz). A beta version of the PDB Archive (https://files-be...

journals.iucr.org

🌟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 ⬇️ www.wwpdb.org/news/news?ye... #PDB

🤖 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/EMBL/job/Hin... #AI #StructuralBiology #Database

Bioinformatician

About the team We are seeking a Bioinformatician with expertise in data integration and experience in structural biology and molecular dynamics (MD) data to join the Velankar team at the European Bioi...

embl.wd103.myworkdayjobs.com

📄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/d...

🚀 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 ⬇️ www.wwpdb.org/news/news?ye... #PDB

Out now in Journal of Applied Crystallography: mmCIF Validator, automated validation of mmCIF files against the PDBx/mmCIF dictionary Useful for structure deposition prep, biocuration, and automated QC (VS Code extension + Python/CLI) Paper: doi.org/10.1107/S160... Code: github.com/PDBeurope/mm...

mmCIF Validator: a comprehensive validation tool for structural biology data files

The mmCIF Validator provides real-time automated validation of mmCIFs against a valid PDBx/mmCIF dictionary. The validator is available as both a Visual Studio Code extension and a standalone Python s...

doi.org

🌟 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⬇️ www.wwpdb.org/news/news?ye...

Closing this weekend! Join us as a scientific biocurator in the OneDep biocuration team. Work with structural data, software and processes that support data deposition and curation. Apply by 2nd Aug: tinyurl.com/47t93kxp. CAK-CDK1-Cyclin-B1: Timing is everything (#cryoEM EMD-54971).

🌟Save time on your next #PDB deposition with the enhanced OneDep "Based on a previous deposition" feature! This feature lets you copy and reuse metadata from a previous deposition, with ORCID support, selective import, and built-in validation. ⬇️more ⬇️ www.wwpdb.org/news/news?ye...

Job alert: Receptors respond to important signalling molecules (#cryoEM EMD-27634) - Our biocurators work directly with scientists to ensure their data are ready for release. Communication is key. Come join the EMDB and OneDep biocuration team. Apply by 2nd Aug: tinyurl.com/47t93kxp

🌟 Events at Microscopy & Microanalysis Join wwPDB members for presentations on the preservation and validation of electron microscopy data at the M&M meeting. 🗓️ August 2-6, 2026 📍 Milwaukee, WI, USA. ⬇️ more ⬇️ 🔗 www.wwpdb.org/news/news?ye... 🔗 mm2026.eventscribe.net #PDB #EM

🚨New PDBe webinar Bringing structural biology to AI: exploring the PDBe MCP servers The session will explore the capabilities offered by the PDBe MCP servers with practical examples. 🗓️ 9 September 2026 🕘 14:30-15:30 (BST) ⬇️ Register here ⬇️ www.ebi.ac.uk/training/eve... #PDB

Job alert: Viruses (#cryoEM EMD-24741), chaperones, molecular assemblies, enzymes, drug targets and more. Structures tell stories. Join the EMDB and OneDep biocuration team at EMBL-EBI and help scientists tell theirs. Apply by 2nd Aug: tinyurl.com/47t93kxp

Explore experimental and predicted macromolecular structures with PDBe tools & resources at our full-day #ECCB2026 tutorial. 📅 3 September 2026 🕘 09:00–17:30 🎤 Ibrahim Roshan & Sri Devan Appasamy 🔗 Register here: eccb2026.org/registration...

Job alert: Protein chaperones ensure proteins fold correctly (#cryoEM EMD-23004). Biocurators ensure structural biology data are accurate and reusable. Join the EMDB and OneDep biocurators to maintain the integrity of structural biology data. Apply by 2nd Aug: tinyurl.com/47t93kxp

🚨 Big PDB changes are one year away Starting July 21, 2027: ▪ PDB Beta Archive becomes the main archive. ▪ Extended PDB IDs and PDBx/mmCIF will be the standard. Start using extended IDs and PDBx/mmCIF today! 🔗 www.wwpdb.org/news/news?ye... #PDB #StructuralBiology

Job alert: Molecular presentation and the adaptive immune response (EMD-45166). Biocurators work closely with software devs, improving and adapting our deposition and curation pipelines. Automation is key. Come join the EMDB and OneDep biocuration team. Apply by 2nd Aug: tinyurl.com/47t93kxp

Job alert: Biology is amazing (EMD-70204). As a biocurator, you get a front-row seat to the structures being deposited in the world’s structural biology databases. Come join the EMDB and OneDep biocuration team. We’re hiring a biocurator. Apply by 2nd Aug: tinyurl.com/47t93kxp

🧬 New @EMBL course: "Protein Domains: Structure, Classification & Evolution" - free & online now. CATH, SCOP, Pfam, IDRs + more. 🔗 www.ebi.ac.uk/training/onl... #StructuralBiology #Bioinformatics #Domains

🚀 Improved support for #3DED/#MicroED is now available in the wwPDB OneDep deposition system! 🔹 New and improved metadata collection 🔹 Required structure factors for validation 🔹 SerialED metadata collection support 🔗 www.wwpdb.org/news/news?ye... #PDB #StructuralBiology

🤖 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/EMBL/job/Hin... #AI #StructuralBiology #Database

Bioinformatician

About the team We are seeking a Bioinformatician with expertise in data integration and experience in structural biology and molecular dynamics (MD) data to join the Velankar team at the European Bioi...

embl.wd103.myworkdayjobs.com

1/2 🎬 That's a wrap on our intro to PDBe MCP Servers. All the videos are now on YouTube - install, usage, Graph Server, and Claude examples - in one playlist. 🎥 www.youtube.com/playlist?lis...

🚀 The PDBe Graph Server is built for power users. Explore the PDBe-KB Neo4j schema with AI-assisted Cypher generation - including nodes, and edges. 🔗 Graph DB: ftp.ebi.ac.uk/pub/databases/msd/graphdb/ #Neo4j #KnowledgeGraph #PDBe #AI #Cypher

🧬 Claude isn't the only AI that can query PDBe. PDBe MCP Servers work with other AI clients too, such as Google Antigravity. You only need one protocol for any MCP-compatible AI. 🎥 Watch the install walkthrough 👇 📦 github.com/PDBeurope/PDBe-MCP-Servers #PDBe #MCP #GoogleAntigravity #AI