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Methods Enzymol. 2016;579:393-412. doi: 10.1016/bs.mie.2016.04.015. Epub 2016 Jun 16.

Databases and Archiving for CryoEM.

Author information

1
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom. Electronic address: ardan@ebi.ac.uk.
2
Research Collaboratory for Structural Bioinformatics, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, United States. Electronic address: cathy.lawson@rutgers.edu.

Abstract

CryoEM in structural biology is currently served by three public archives-EMDB for 3DEM reconstructions, PDB for models built from 3DEM reconstructions, and EMPIAR for the raw 2D image data used to obtain the 3DEM reconstructions. These archives play a vital role for both the structural community and the wider biological community in making the data accessible so that results may be reused, reassessed, and integrated with other structural and bioinformatics resources. The important role of the archives is underpinned by the fact that many journals mandate the deposition of data to PDB and EMDB on publication. The field is currently undergoing transformative changes where on the one hand high-resolution structures are becoming a routine occurrence while on the other hand electron tomography is enabling the study of macromolecules in the cellular context. Concomitantly the archives are evolving to best serve their stakeholder communities. In this chapter, we describe the current state of the archives, resources available for depositing, accessing, searching, visualizing and validating data, on-going community-wide initiatives and opportunities, and challenges for the future.

KEYWORDS:

Databases; EMDB; EMDataBank; EMPIAR; Protein Data Bank; Validation

PMID:
27572735
PMCID:
PMC5351295
DOI:
10.1016/bs.mie.2016.04.015
[Indexed for MEDLINE]
Free PMC Article

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