Abstract
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.
Highlights
The Protein Data Bank (PDB, [1]) is the single global archive of experimentally determined three-dimensional (3D) structures of biological macromolecules and their complexes
The wwPDB partners collaborate on the annotation of macromolecular structure depositions and release new data into the PDB archive each week
Since 2015, the wwPDB partners have used a unified system for deposition, curation and validation of the deposited structure data, called OneDep, with Protein Data Bank in Europe (PDBe) being responsible for the annotation of all depositions from European and African institutions [7]
Summary
The Protein Data Bank (PDB, [1]) is the single global archive of experimentally determined three-dimensional (3D) structures of biological macromolecules and their complexes. This includes logically grouping information to provide relevant context on PDBe Web pages, and developing programmatic access to the underlying data for bioinformatics use cases.
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