Protein Data Bank

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

[Protein Data Bank @PDBeurope]

🚀 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:
https://t.co/3dsJzPpAEh

#Neo4j #KnowledgeGraph #PDBe #AI #Cypher

[Protein Data Bank @PDBeurope]

🧬 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 👇

📦 https://t.co/NcwR2h1ipu

#PDBe #MCP #GoogleAntigravity

[Protein Data Bank @PDBeurope]

🧬 New tutorial video drop from @EMBL_EBI!

"Similarity Metrics & Confidence Scores in Protein Structure Prediction" by Dr. Yonathan Goldtzvik- Essential for anyone using #AlphaFold 🎯

🎥 https://t.co/ZIgv9CXPLB

#StructuralBiology #Bioinformatics #ProteinStructure #pLDDT

[Protein Data Bank @PDBeurope]

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”

📦 https://t.co/NcwR2h1ipu

#PDBe #MCP #ClaudeAI #Bioinformatics

[Protein Data Bank @PDBeurope]

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

[Protein Data Bank @PDBeurope]

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

[Protein Data Bank @PDBeurope]

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 👇

[Protein Data Bank @PDBeurope]

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.

[Protein Data Bank @PDBeurope]

Read more in the full news announcement: https://t.co/NvZOtE7HmS

[Protein Data Bank @PDBeurope]

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: https://t.co/hxH79eWZsy

[Protein Data Bank @PDBeurope]

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:
https://t.co/abkDFOwMeD

[Protein Data Bank @PDBeurope]

🚨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)

🔗https://t.co/mhoFAHCwbX

#PDB

[Protein Data Bank @PDBeurope]

🚨July 21, 2027: PDB Beta Archive replaces current PDB archive.

Key updates:
• Extended IDs (1ABC → pdb_00001abc).
• Only 12-char IDs issued.
• Data in PDBx/mmCIF & PDBML only.

All PDB users must transition to extended IDs and PDBx/mmCIF.

🔗https://t.co/LpXTcAkYdi

#PDB

[Protein Data Bank @PDBeurope]

🚨Updated Validation Reports for Released PDB and EMDB Entries.

Key highlights:
• Recalculated percentiles for all entries.
• New stats reflecting PDB archive as of Dec 31, 2025.
• Added Q-score percentiles.
• Improved ligand validation.

🔗https://t.co/k9DPckqhWW

#PDB

[Protein Data Bank @PDBeurope]

@mitsenkov, Senior Bioinformatician at AlphaFold DB, will be giving a keynote talk for @EHA_Hematology Computational Biology Training in Hematology programme, speaking with haematologists about structural biology and practical AlphaFold DB use-cases.

#AlphaFold #EHA2026

[Protein Data Bank @PDBeurope]

An honour to participate with works from the PDBArt project in the exhibition "Habitar lo Invisible" (Inhabiting the Invisible), organised by BioScience-App in Ayacucho, Peru.

⬇️ more ⬇️
https://t.co/Njc7L2rRSs

https://t.co/s5hOvXJNIf

#science #artㅤ

[EMDB - EMPIAR @EBI @EMDB_EMPIAR]

🚨 Job alert 🚨: Every published #cryoEM structure is paired with access to its underlying data. Want to help make that possible? Join the OneDep biocuration team at EBI as an EMDB biocurator: https://t.co/c5aTSYCPlV