Abstract
The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed.
Highlights
The Electron Microscopy Data Bank (EMDB; Tagari et al (2002)) archive was established at the European Bioinformatics Institute (EBI) in 2002 as a means of making 3D macromolecular reconstructions derived from 3D electron microscopy (3DEM) experiments freely and publicly available
3DEM maps and models can be deposited at Protein Data Bank in Europe (PDBe), RCSB and the Protein Data Bank Japan (PDBj)
The deposited 3DEM data is stored in the EMDB ftp archive at EBI and from there redistributed together with the PDB archive through the ftp sites of the Worldwide Protein Data Bank partners
Summary
The Electron Microscopy Data Bank (EMDB; Tagari et al (2002)) archive was established at the European Bioinformatics Institute (EBI) in 2002 as a means of making 3D macromolecular reconstructions derived from 3D electron microscopy (3DEM) experiments freely and publicly available. It has since become the authoritative global archive for such data, comprising over 2000 released maps (October 2013) derived from a range of 3DEM techniques including single-particle reconstruction, helical reconstruction, tomography and electron crystallography. In 2012, over 400 new maps were released.
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