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

Saqib Mir(European Bioinformatics Institute), Younes Alhroub(European Bioinformatics Institute), Stephen Anyango(European Bioinformatics Institute), David Armstrong(European Bioinformatics Institute), John M. Berrisford(European Bioinformatics Institute), Alice R. Clark(European Bioinformatics Institute), M.J. Conroy(European Bioinformatics Institute), Jose M Dana(European Bioinformatics Institute), Mandar Deshpande(European Bioinformatics Institute), Deepti Gupta(European Bioinformatics Institute), Aleksandras Gutmanas(European Bioinformatics Institute), P Haslam(European Bioinformatics Institute), Lora Mak(European Bioinformatics Institute), Abhik Mukhopadhyay(European Bioinformatics Institute), Nurul Nadzirin(European Bioinformatics Institute), Typhaine Paysan‐Lafosse(European Bioinformatics Institute), David Sehnal(Central European Institute of Technology), Sanchayita Sen(European Bioinformatics Institute), Oliver S. Smart(European Bioinformatics Institute), Mihály Váradi(European Bioinformatics Institute), Gerard J. Kleywegt(European Bioinformatics Institute), Sameer Velankar(European Bioinformatics Institute)
Nucleic Acids Research
October 26, 2017
10.1093/nar/gkx1070
Cited by 85Open Access
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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.

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