PDBe EMBL-EBI

This repository provides a set of easy-to-use tools for generating the required files and metadata to seamlessly integrate your models into AFDB.

The PDB RNA viewer depicts the secondary structure of a RNA in a 2D representation

Residue contacts viewer in Protein Contacts Atlas

PDB ProtVista Viewer

Generates images from mmCIF/BCIF files

Public repository of the PDBe ligand environment component

Summary web-component for the PDB 3D complex, a server that analyses the complexes in crystal structures

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.

Identifies relevant ligands in the PDB