PDBe-KB: collaboratively defining the biological context of structural data

Abstract

The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.

Figure 1.

Schematic overview of the PDBe-KB infrastructure. PDBe-KB partner resources convert their annotations to a predefined JSON format and transfer these file sets via FTP. Weekly data validation and integration processes parse and load the annotations into the PDBe graph database. A rich set of API endpoints expose the data and power the PDBe-KB aggregated views. Researchers can access the data by setting up a local instance of the graph database, using the API endpoints, or visiting the aggregated view pages.

Figure 2.

Superposition of protein chains and ligand molecules. The aggregated views of proteins provide access to superposed protein segments and offer a display mode that overlays all the observed ligands on representative chains from superposition clusters. The figure displays the ligand superposition of all the available small molecules in PDB structures of the 3C-like proteinase nsp5 of SARS-CoV-2.

Figure 3.

Bulk data download service. The aggregated views of proteins provide a graphical user interface to a new bulk data download service which enables researchers to download all the coordinates, sequences and validation data available for a protein of interest.

Figure 4.

Processed proteins section. The aggregated views of proteins now include a section highlighting all the mature, processed proteins for a polyprotein. In addition, users can click on the green boxes to view the 3D structures using Mol*, and they can navigate to dedicated processed proteins pages by clicking on the ‘view page’ button.

Figure 5.

Predicted models of a protein of interest. The aggregated views of proteins now provide an overview of available predicted models from data resources such as AlphaFold DB and SWISS-MODEL.

Figure 6.

Ligand annotations. The aggregated views of proteins now display annotations for ligand molecules based on a cofactor data pipeline. Similarly, we annotate peptides and antibodies in the macromolecular interactions section.