Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB

Lagerstedt, Ingvar; Moore, William J.; Patwardhan, Ardan; Sanz-García, Eduardo; Best, C.; Swedlow, Jason R.; Kleywegt, Gerard J.

doi:10.1016/j.jsb.2013.09.021

Cited by 35 publications

(55 citation statements)

References 42 publications

(52 reference statements)

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“…It is well known that even today there are often issues with the reliability of ligands modelled inside structures deposited in the PDB, so such tools are tremendously useful. For EMDB entries, there are also a variety of interactive and static displays of information that have been designed to help users assess their quality as well as the quality of the corresponding fitted PDB model (if there is one) [56]. …”

Section: The Future Is Bright and Multi-scalarmentioning

confidence: 99%

Structural biology data archiving – where we are and what lies ahead

2018

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For almost 50 years, structural biology has endeavoured to conserve and share its experimental data and their interpretations (usually, atomistic models) through global public archives such as the Protein Data Bank, Electron Microscopy Data Bank and Biological Magnetic Resonance Data Bank (BMRB). These archives are treasure troves of freely accessible data that document our quest for molecular or atomic understanding of biological function and processes in health and disease. They have prepared the field to tackle new archiving challenges as more and more (combinations of) techniques are being utilized to elucidate structure at ever increasing length scales. Furthermore, the field has made substantial efforts to develop validation methods that help users to assess the reliability of structures and to identify the most appropriate data for their needs. In this Review, we present an overview of public data archives in structural biology and discuss the importance of validation for users and producers of structural data. Finally, we sketch our efforts to integrate structural data with bioimaging data and with other sources of biological data. This will make relevant structural information available and more easily discoverable for a wide range of scientists.

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Section: The Future Is Bright and Multi-scalarmentioning

confidence: 99%

Structural biology data archiving – where we are and what lies ahead

2018

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“…First, a Java-applet-based volume viewer permits 3D visualization of maps and their associated PDB coordinate models (Lagerstedt et al, 2013; Lawson et al, 2011). Second, a volume slicer is available for inspecting 2D slices of EMDB entries from three orthogonal orientations (Salavert-Torres et al, 2016).…”

Section: Resourcesmentioning

confidence: 99%

“…Second, a volume slicer is available for inspecting 2D slices of EMDB entries from three orthogonal orientations (Salavert-Torres et al, 2016). Third, visual analysis pages (Gutmanas et al, 2014; Lagerstedt et al, 2013; Patwardhan et al, 2012) facilitate analysis and validation of maps, tomograms and models by providing static images of map orthogonal projections and central slices as well as graphs of FSC curves, map density distribution, rotationally averaged power spectrum, volume estimation vs. contour level, and model atom inclusion at the recommended contour level. These visualization tools have been designed to help non-experts and experts alike to gain insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialized software or to download large amounts of data from the structural data archives.…”

Section: Resourcesmentioning

confidence: 99%

Databases and Archiving for CryoEM

Patwardhan

Lawson²

2016

Methods in Enzymology

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Cryo-EM 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, visualising and validating data, on-going community-wide initiatives and opportunities and challenges for the future.

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“…These charts are useful for basic data mining purposes, for instance to view trends in instrument usage or to view resolution trends among EMDB entries. Basic Protocol 7 shows the use of the 'Visual Analysis' pages to perform a basic assessment of EMDB entries (Lagerstedt et al, 2013). The Visual Analysis pages present image representations of the structures as well as various pre-calculated analytical charts.…”

Section: Introductionmentioning

confidence: 99%

EMDB Web Resources

Abbott

Iudin

Korir

et al. 2018

CP in Bioinformatics

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The Electron Microscopy Data Bank (EMDB; http://emdb-empiar.org) is a global openly-accessible archive of biomolecular and cellular 3D reconstructions derived from electron microscopy (EM) data. EMBL-EBI develops web-based resources to facilitate the reuse of EMDB data. Here we provide protocols for how these resources can be used for searching EMDB, visualising EMDB structures, statistically analysing EMDB content and checking the validity of EMDB structures. Protocols for searching include quick link categories from the main page, links to latest entries released during the weekly cycle, filtered browsing of the entire archive and a form-based search. For visualisation, the 'Volume Slicer' enables slices of EMDB entries to be visualised interactively and in three orthogonal directions. The web service (https://emdb-empiar.org/emstats) provides up-to-date interactive statistical charts analysing EMDB. All EMDB entries have 'visual analysis' pages that provide basic validation information for the entry.

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Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB

Cited by 35 publications

References 42 publications

Structural biology data archiving – where we are and what lies ahead

Structural biology data archiving – where we are and what lies ahead

Databases and Archiving for CryoEM

EMDB Web Resources

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