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 assistance for intelligent Cypher query generation, bridging structural biology and AI research.

A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

Notebook-Driven Development to nurture new features supported and maintained by our diverse user base.

A Python-based pipeline to wrap around a transformer model to annotated IUCr-style JATS XML for functional protein residues

Public repository of the PDBe ligand environment component

Real-time VSCode extension and standalone Python script for validating mmCIF/CIF files against the PDBx/mmCIF dictionary or any CIF dictionary.