@PDBeurope profile picture
Protein Data Bank @PDBeurope

PDBe is a founding member of the wwPDB. The PDBe team is also responsible for the PDBe-KB, AlphaFold DB and 3D Beacons resources.

Joined October 2010
  • Posts 7,722
  • Following 791
  • Followers 22,177
3,393 Photos and videos
🧬 New @EMBL course: "Protein Domains: Structure, Classification & Evolution" - free & online now. CATH, SCOP, Pfam, IDRs more. 🔗 ebi.ac.uk/training/online/co… #StructuralBiology #Bioinformatics #Domains
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🚀 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 🔗 wwpdb.org/news/news?year=202… #PDB #StructuralBiology
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🤖 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
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2/2 What's in the playlist: ▶ How to install the servers ▶ Using MCP in practice ▶ Graph Server walkthrough ▶ Asking Claude about protein structures 📦 github.com/PDBeurope/PDBe-MC… #PDBe #MCP #StructuralBiology #AI

GitHub - PDBeurope/PDBe-MCP-Servers: PDBe MCP Servers integrate Protein Data Bank Europe resources...

PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema as...

github.com
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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. 🎥youtube.com/playlist?list=PL…

PDBe MCP servers

youtube.com
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🚀 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/… #Neo4j #KnowledgeGraph #PDBe #AI #Cypher
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🧬 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-MC… #PDBe #MCP #GoogleAntigravity
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🧬 New tutorial video drop from @EMBL_EBI! "Similarity Metrics & Confidence Scores in Protein Structure Prediction" by Dr. Yonathan Goldtzvik- Essential for anyone using #AlphaFold 🎯 🎥 youtu.be/dVFHr0ZV4-0 #StructuralBiology #Bioinformatics #ProteinStructure #pLDDT

Similarity Metrics & Confidence Scores in Protein Structure Prediction | EMBL-EBI Tutorial

This tutorial developed by Dr. Yonathan Goldtzvik (EMBL-EBI) provid...

youtube.com
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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-MC… #PDBe #MCP #ClaudeAI #Bioinformatics
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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 #MCP
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6/6 Built at @EBI_EMBL by Sreenath Sasidharan Nair 💙 Apache 2.0 · Python 3.10 We’d love to see what the community builds next. #PDBe #MCP #ModelContextProtocol #StructuralBiology #AI
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5/6 What can you build with it? → Ask Claude about any PDB entry in plain English. → Generate Cypher queries with schema awareness. → Build structural biology copilots. → Create lab assistants powered by live PDBe data. → Explore protein structure graphs interactively.
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4/6 Get started in under a minute: uvx pdbe-mcp-server Works with Claude Desktop on macOS, Windows, and Linux. 📦 PyPI: pypi.org/project/pdbe-mcp-se… 💻 GitHub: github.com/PDBeurope/PDBe-MC…

pdbe-mcp-server

A Model Context Protocol (MCP) server for accessing PDBe (Protein Data Bank in Europe) structural biology data and services

pypi.org
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3/6 PDBe MCP Servers provide AI access to: ⚡ API Server — biological structure data via REST 🔍 Search Server — Solr-powered schema-aware search 🌐 Graph Server — Neo4j schema Cypher query generation One protocol. Three servers. Infinite possibilities.
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2/6 LLMs can describe protein structures. But until now, they couldn’t actually access PDBe’s live data. No fresh depositions. No schema-aware search. No graph exploration. No structured retrieval. So we built the bridge.
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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 👇
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Read more in the full news announcement: ebi.ac.uk/about/news/updates…

PDBe-SIFTS for protein sequence-structure mapping

First open-source release of SIFTS for residue-level mapping between protein sequences and structures

ebi.ac.uk
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PDBe-SIFTS is now open source 🎉 Developed in collaboration with @PDBeurope 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/SIFTS
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Our bioRxiv paper 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: biorxiv.org/content/10.64898…
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🚨New Syntax for PDB DOIs for Entries Released After July 21, 2027 • New entries DOI will use extended ID (e.g. 10.2210/pdb_1000axyz/pdb) • Older entries keep 4-character DOI format (e.g. 10.2210/pdb1abc/pdb) 🔗wwpdb.org/news/news?year=202… #PDB
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