New electron microscopy database and deposition system

Tagari, Mohamed; Newman, Richard; Chagoyen, Mónica; Carazo, José Marı́a; Henrick, Kim

doi:10.1016/s0968-0004(02)02176-x

Cited by 138 publications

(109 citation statements)

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“…The MRC file format is one of the principal formats for cryo-EM data, and is used in common programs such as RELION (Scheres et al, 2008) and for the deposition of experimental volumes in the EMDB (Tagari et al, 2002;Lawson et al, 2016). Closely related to the CCP4 map format, it can be used to store individual micrographs, stacks of twodimensional images, three-dimensional volumes and stacks of three-dimensional volumes.…”

Section: Python Mrc File Librarymentioning

confidence: 99%

Recent developments in theCCP-EMsoftware suite

Burnley

Palmer

Winn

2017

Acta Crystallogr D Struct Biol

340

301

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As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryoMicroscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessible via a user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The current CCP-EM suite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail.

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Section: Python Mrc File Librarymentioning

confidence: 99%

Recent developments in theCCP-EMsoftware suite

Burnley

Palmer

Winn

2017

Acta Crystallogr D Struct Biol

340

301

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“…PDBe is also committed to delivering these data back to the community in forms that encourage further developments in the field of biomacromolecular NMR spectroscopy. Since 2002, PDBe has worked closely with the EM community in establishing and developing the Electron Microscopy Data Bank (EMDB; Tagari et al, 2002). Initially a purely European affair, the archive is now operated and developed jointly by the three EMDB partner sites PDBe, RCSB and BCM.…”

Section: Experimental Datamentioning

confidence: 99%

“…Under the leadership of Geoff Barton (1998Barton ( -2001 and Kim Henrick (2001, PDBe built up a reputation as a provider of advanced structural bioinformatics databases and services. PDBe also founded the Electron Microscopy Data Bank (EMDB; http://emdatabank.org; Tagari et al, 2002;Henrick et al, 2003) in 2002. However, like the PDB, EMDB is now an international collaborative effort involving PDBe, RCSB and the laboratory of Wah Chiu at Baylor College of Medicine (BCM) (Lawson et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

The Protein Data Bank in Europe (PDBe): bringing structure to biology

Velankar

Kleywegt

2011

Acta Crystallogr D Biol Cryst

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The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions of X‐ray, NMR and EM data and structure models. PDBe also provides advanced bioinformatics services based on data from the PDB and related resources. Some of the challenges facing the PDB and its guardians are discussed, as well as some of the areas on which PDBe activities will focus in the future (advanced services, ligands, integration, validation and experimental data). Finally, some recent developments at PDBe are described.

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“…The wwPDB partner sites collaborate on 'data-in' activities, including deposition and annotation software and policies to ensure the availability of a uniform archive. The deposition and annotation of macromolecular structure data for the PDB and the Electron Microscopy Data Bank (EMDB; Tagari et al, 2002;Lawson et al, 2011), which archives the electric potential maps from 3DEM experiments, ISSN 2059-7983 is managed using the recently launched OneDep system .…”

Section: Introductionmentioning

confidence: 99%

Worldwide Protein Data Bank validation information: usage and trends

Smart

Horský

Gore

et al. 2018

Acta Crystallogr D Struct Biol

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Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrends DB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

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New electron microscopy database and deposition system

Cited by 138 publications

References 0 publications

Recent developments in theCCP-EMsoftware suite

Recent developments in theCCP-EMsoftware suite

The Protein Data Bank in Europe (PDBe): bringing structure to biology

Worldwide Protein Data Bank validation information: usage and trends

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