All the annotations provided by PDBe-KB partners are integrated with core PDBe data in a massive graph database which is implemented in Neo4J.

In this graph each PDB entry is represented as a tree, with the root being the PDB entry, connected to chains and entities, which are then connected to residues. Each of the PDB residues (>150 million) are linked to available annotations (e.g. is the residue part of a catalytic site?, or is it on a macromolecular interaction interface?) and are also directly connected to their corresponding UniProt residues. Storing PDBe-KB data as a graph offers great benefits in particular by allowing straightforward transfer of annotations between PDB entries which map to the same UniProt accession, as well as to highly identical UniProt accession.

PDBe API is powered by this graph database which is consumed by different PDBe-KB aggregated views. This database can also be used as a powerful research tool by diving deep into the underlying relationships. Check out the Download section for downloading the database for in-house use.

To effectively explore the database, it is necessary to refer to the schema of the underlying data.