Protein Data Bank in Europe (PDBe)
@pdbeurope
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
🌟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...
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...
🧬 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
🚀 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
Connect Claude to PDBe in 3 steps: 1️⃣ Install uv 2️⃣ Run: uvx pdbe-mcp-server --server-type pdbe_api_server 3️⃣ Add config to Claude Desktop Now ask: “Find X-ray structures for UniProt P12345” 📦 github.com/PDBeurope/PDBe-MCP-Servers #PDBe #MCP #ClaudeAI #Bioinformatics
What’s inside the PDBe MCP package? ⚡ API Server Live structural biology data via REST-powered MCP tools 🔍 Search Server Schema-aware Solr search across PDBe 🌐 Graph Server Neo4j schema exploration + Cypher generation One install. Three servers. Unlimited workflows. #PDBe #MCP #Bioinformatics
1/6 🧪 Big news for structural biology and AI: PDBe is now AI-native. We’ve built MCP Servers that connect the Protein Data Bank in Europe and the Alphafold Protein Structure Database directly to Claude and other MCP-compatible AI systems. Here’s what that unlocks 👇
PDBe-SIFTS is now open source 🎉 Developed in collaboration with PDBe (@pdbeurope.bsky.social) and UniProt, it enables fast, accurate residue-level mapping between protein sequences and structures, achieving >93% agreement with curated mappings. Get started: github.com/PDBeurope/SI...
Our new bioRxiv preprint introduces ECIFP: a scalable interaction fingerprint that maps the landscape of ligand binding modes. ✅Identified binding modes for 9k+ ligands ✅Analysis of 48k+ binding sites from 21k+ proteins ✅Open-source & interpretable ⬇️ more ⬇️ www.biorxiv.org/content/10.6... #PDB
@mitsenkov.bsky.social , Senior Bioinformatician at AlphaFold DB, will be giving a keynote talk for EHA’s Computational Biology Training in Hematology programme, speaking with haematologists about structural biology and practical AlphaFold DB use-cases. #AlphaFold #EHA2026
Custom dictionary support is available in the PDBe mmCIF validator: VS Code: set dictionary path in settings Python script: pass dictionary path via CLI #mmCIF #PDB #Bioinformatics #StructuralBiology
𝗣𝗗𝗕𝗲 𝗘𝗻𝘁𝗿𝘆 𝗣𝗮𝗴𝗲𝘀 just got better! 🚀 🔹 New tab with links to partner and related databases 🔹 PDBe extended codes now displayed 🔹 More data fields requested by the community Explore an entry: pdbe.org/12ca We need your feedback! More updates are coming!
Huge thanks to @nextflow.io & @seqera.io for fantastic hackathons to support reproducible workflows! Big shout‑out to volunteers Yunjia Zhang (from Sanger Institute), @vagkaratzas.bsky.social & @mberacochea.bsky.social (from @ebi.embl.org) for hands-on learning with the PDBe team. ✨💖 #opensource
𝗣𝗗𝗕𝗲 𝗺𝗺𝗖𝗜𝗙 𝗩𝗮𝗹𝗶𝗱𝗮𝘁𝗼𝗿: validate your mmCIF files against PDBx/mmCIF dictionary ✅ Real-time check ✅ Metadata completeness indicator pip install pdbe-mmcif-validator install VS code extension: marketplace.visualstudio.com/items?itemNa... GitHub - PDBeurope/mmcif-validator: github.com/PDBeurope/mm...
Register for PDB Workshops at IUCr2026: Pre-meeting workshop: Enhancing PDB Deposition and Validation Practices 🗓️𝐀𝐮𝐠𝐮𝐬𝐭 𝟏𝟎, 𝟐𝟎𝟐𝟔 Enabling PDB Deposition of Integrative/Hybrid Methods Structures. 🗓️𝐀𝐮𝐠𝐮𝐬𝐭 𝟏𝟏, 𝟐𝟎𝟐𝟔 🔗https://www.wwpdb.org/news/news?year=2026#69b2b76a8557ae0f261bc715
The Protein Data Bank (#PDB) has reached a new milestone: 250,441 entries in the archive, a record since its founding in 1971, all thanks to the efforts and contributions of the structural biology community. ⬇️ more ⬇️ www.wwpdb.org/news/news?ye... #StructuralBiology
We’re running a survey to learn about 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
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...
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
🎄✨ 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...
🚀 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