PDBe-KB: a community-driven resource for structural and functional annotations

Abstract

Abstract The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macromolecular structure data, contained in the Protein Data Bank (PDB). The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research. Here, we describe the guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembled data, and programmatic access endpoints. We also describe a series of novel web-pages—the PDBe-KB aggregated views of structure data—which combine information on macromolecular structures from many PDB entries. We have recently released the first set of pages in this series, which provide an overview of available structural and functional information for a protein of interest, referenced by a UniProtKB accession.

Keywords

Affiliated Institutions

• Institute of Structural and Molecular Biology GB
• University of Dundee GB
• Cresset (United Kingdom) GB
• University of Cambridge GB
• Institute of Cancer Research GB
• King's College London GB
• European Molecular Biology Laboratory DE
• University College London GB
• University of Luxembourg LU
• Vrije Universiteit Brussel BE
• Centre for Genomic Regulation ES
• Universitat Politècnica de Catalunya ES
• University of Kent GB
• Weizmann Institute of Science IL
• University of Georgia US
• European Bioinformatics Institute GB
• University of Rome Tor Vergata IT
• Cancer Research UK GB
• Palacký University Olomouc CZ
• Central European Institute of Technology CZ
• Indian Institute of Science Education and Research Pune IN
• Charles University CZ
• Imperial College London GB
• Barcelona Supercomputing Center ES
• Central European Institute of Technology – Masaryk University CZ

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