**
*Hi everyone,*
*
We wanted to share something new from PDBe / EMBL-EBI that might be
interesting to the CCP4 community.
We’ve recently released a set of PDBe MCP (Model Context Protocol)
serversthat allow AI tools like Claude and other AI MCP-compatible
assistants to interact directly with live structural biology data from PDBe.
In practice, this means AI assistants can now:
*
search PDBe structures conversationally
*
access up-to-date structural biology data
*
explore graph relationships
*
help generate schema-aware queries
*
assist with structural biology workflows directly inside AI-enabled
tools
We currently provide three MCP servers:
⚡ API Server— access PDBe structural data via REST-backed tools🔍 Search
Server— schema-aware Solr search across PDBe🌐 Graph Server— Neo4j
schema exploration + Cypher query generation
A few example prompts:
*
“Find cryo-EM kinase structures under 3.5 Å”
*
“Show structures linked to UniProt P12345”
*
“Generate a Cypher query for ligand interactions”
The goal is to make structural biology data easier to explore
programmatically and conversationally — especially for researchers,
developers, and bioinformatics workflows.
Everything is open source:
GitHub:https://github.com/PDBeurope/PDBe-MCP-Servers<https://github.com/PDBeurope/PDBe-MCP-Servers>PyPI:https://pypi.org/project/pdbe-mcp-server/
<https://pypi.org/project/pdbe-mcp-server/>
Install is very simple:
uvx pdbe-mcp-server
We’d love feedback from the CCP4 community, especially from anyone
experimenting with AI-assisted structural biology workflows.
Happy to answer questions or hear ideas for additional features/use cases 🙂
Best regards,*
*Deborah Harrus, on behalf of the PDBe team*
--
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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