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Nucleic Acids Res. 2018 Jan 4;46(D1):D486-D492. doi: 10.1093/nar/gkx1070.

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.

Author information

1
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
2
InterPro, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
3
CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic.

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.

PMID:
29126160
PMCID:
PMC5753225
DOI:
10.1093/nar/gkx1070
[Indexed for MEDLINE]
Free PMC Article

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