Aggregated views
PDBe-KB Aggregated Views are a set of web pages that aggregate all the structural and functional data for a specific molecular entity. There are many possible and valuable ways to aggregate data, for example by proteins, domains, small molecules or macromolecular complexes.
Aggregated views of proteins
Structures
Small-molecules
Macromolecular Interactions
Functional Annotations
The PDBe-KB Aggregated View of proteins provides a comprehensive overview of structural data available in the PDB for a full-length protein sequence (i.e. UniProt accession). Either PDB identifiers or UniProt accessions can be used to display all the available data for a given protein. The webpages display a list of PDB entries containing the protein, small and macromolecules and their interaction sites with the given protein, and additional functional annotations, such as sequence conservation and druggable sites. See example for breast cancer type 1 susceptibility protein (P38398)
3D-Beacons Network
3D-Beacons Network is an open collaboration between providers of macromolecular structure models. It provides access to model coordinates and meta-information from all the contributing data resources in a standardised data format.
The 3D-Beacons portal allows users to search using UniProt accessions and see all the available experimental and computational models from the member data providers.
See example for UniProt accession P38398 (BRCA1_HUMAN)
The PDBe-KB Aggregated Views of proteins displays these structures for a protein of interest.
See example for breast cancer type 1 susceptibility protein (P38398)
Varadi M, Nair S, et al., 3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources , GigaScience, Volume 11, 2022
Graph database
All the annotations provided by PDBe-KB partners are integrated with the core PDBe data in a knowledge graph using a graph database powered by Neo4j. This graph database can be freely downloaded, installed and queried locally.
API
The REST API provides programmatic access to PDBe-KB annotations. It provides endpoints specific calls to access aggregated data from across all the relevant PDB entries, for example based on entities, Uniprot IDs, residues and more.
PDBe-KB component library
Our reusable data visualisation web components are publicly available from GitHub. These repositories include the 2D sequence feature viewer, PDB ProtVista, and web components used on the various aggregated views. All code is available under Apache 2.0 license.
Public FTP area
FTP access to PDBe-KB data including annotations, benchmarking datasets and superposition data.
Other services
PDBe and PDBe-KB provide many other services from data analysis to programmatic access and data visualisation.