scholarly journals New wwPDB validation pipelines for X-ray, NMR and 3DEM structures

2014 ◽  
Vol 70 (a1) ◽  
pp. C1478-C1478
Author(s):  
Swanand Gore ◽  
Pieter Hendrickx ◽  
Eduardo Sanz-Garcia ◽  
Sameer Velankar ◽  
Gerard Kleywegt
Keyword(s):  
Electron Microscopy ◽  
Protein Data Bank ◽  
Data Bank ◽  
X Ray ◽  
Task Forces ◽  
Annotation System ◽  
Electron Microscopy Data ◽  
Microscopy Data ◽  
Machine Readable

The Protein Data Bank (PDB) is the single global archive of 3D biomacromolecular structure data. The archive is managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org) organisation through its partners, the Research Collaboratory for Structural Bioinformatics (RCSB PDB), the Protein Data Bank Japan (PDBj), the Protein Data Bank in Europe and the Biological Magnetic Resonance Bank (BMRB). Analogously, the Electron Microscopy Data Bank (EMDB) is managed by the EMDataBank (emdatabank.org) organisation. A few years ago, realising the needs and opportunities to assess the quality of biomacromolecular structures deposited in the PDB, the wwPDB and EMDataBank partners established Validation Task Forces (VTFs) to advice them on up-to-date and community-agreed methods and standards to validate X-ray, NMR and 3DEM structures and data. All three VTFs have now published their recommendations (1, 2, 3) and these are getting implemented as validation-software pipelines . The pipelines are integrated in the new joint wwPDB deposition and annotation system (http://deposit.wwpdb.org/deposition/). In addition, stand-alone servers are provided to allow practising structural biologists to validate models prior to publication and deposition (http://wwpdb.org/validation-servers.html). The validation pipelines and the output they produce (human-readable PDF reports and machine-readable XML files) will be described.

scholarly journals New tools for the analysis and validation of cryo-EM maps and atomic models

2018 ◽  
Vol 74 (9) ◽  
pp. 814-840 ◽  
Author(s):  
Pavel V. Afonine ◽  
Bruno P. Klaholz ◽  
Nigel W. Moriarty ◽  
Billy K. Poon ◽  
Oleg V. Sobolev ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Protein Data Bank ◽  
Computational Methods ◽  
Data Bank ◽  
Macromolecular Crystallography ◽  
Electron Cryomicroscopy ◽  
New Methods ◽  
Atomic Models ◽  
Electron Microscopy Data ◽  
Microscopy Data

Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented inPHENIXare discussed, includingd99to estimate resolution,phenix.auto_sharpento improve maps andphenix.mtriageto analyze cryo-EM maps. It is suggested that cryo-EM half-maps and masks should be deposited to facilitate the evaluation and validation of cryo-EM-derived atomic models and maps. The application of these tools to deposited cryo-EM atomic models and maps is also presented.

scholarly journals Worldwide Protein Data Bank validation information: usage and trends

2018 ◽  
Vol 74 (3) ◽  
pp. 237-244 ◽  
Author(s):  
Oliver S. Smart ◽  
Vladimír Horský ◽  
Swanand Gore ◽  
Radka Svobodová Vařeková ◽  
Veronika Bendová ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Three Dimensional ◽  
Data Bank ◽  
Resonance Spectroscopy ◽  
X Ray ◽  
Validation Metrics ◽  
Task Forces ◽  
X Ray Crystallography ◽  
Structure Properties

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 ValTrendsDBdatabase 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.

scholarly journals Implementing an X-ray validation pipeline for the Protein Data Bank

2012 ◽  
Vol 68 (4) ◽  
pp. 478-483 ◽  
Author(s):  
Swanand Gore ◽  
Sameer Velankar ◽  
Gerard J. Kleywegt
Keyword(s):  
Protein Data Bank ◽  
Structural Data ◽  
Data Bank ◽  
Software Pipeline ◽  
X Ray ◽  
Validation Methods ◽  
Task Forces ◽  
Related Information ◽  
Ongoing Work

There is an increasing realisation that the quality of the biomacromolecular structures deposited in the Protein Data Bank (PDB) archive needs to be assessed critically using established and powerful validation methods. The Worldwide Protein Data Bank (wwPDB) organization has convened several Validation Task Forces (VTFs) to advise on the methods and standards that should be used to validate all of the entries already in the PDB as well as all structures that will be deposited in the future. The recommendations of the X-ray VTF are currently being implemented in a software pipeline. Here, ongoing work on this pipeline is briefly described as well as ways in which validation-related information could be presented to users of structural data.

scholarly journals New tools for the analysis and validation of Cryo-EM maps and atomic models

2018 ◽  
Author(s):  
Pavel V. Afonine ◽  
Bruno P. Klaholz ◽  
Nigel W. Moriarty ◽  
Billy K. Poon ◽  
Oleg V. Sobolev ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Protein Data Bank ◽  
Computational Methods ◽  
Data Bank ◽  
Macromolecular Crystallography ◽  
New Methods ◽  
Atomic Models ◽  
Electron Microscopy Data ◽  
Recent Advances ◽  
Microscopy Data

AbstractRecent advances in the field of electron cryo-microscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of bio-macromolecules solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically for cryo-EM validation are required. We discuss new computational methods and tools implemented in Phenix, including d99 to estimate resolution, phenix.auto_sharpen to improve maps, and phenix.mtriage to analyze cryo-EM maps. We suggest that cryo-EM half-maps and masks are deposited to facilitate evaluation and validation of cryo-EM derived atomic models and maps. We also present the application of these tools to deposited cryo-EM atomic models and maps.

VASEM: visual analytics system for electron microscopy data bank

2019 ◽  
Vol 22 (6) ◽  
pp. 1145-1159 ◽  
Author(s):  
Jun Liu ◽  
Yang Gao ◽  
Guihua Shan ◽  
Xuebin Chi
Keyword(s):  
Electron Microscopy ◽  
Visual Analytics ◽  
Data Bank ◽  
Electron Microscopy Data ◽  
Microscopy Data

scholarly journals Trends in the Electron Microscopy Data Bank (EMDB)

2017 ◽  
Vol 73 (6) ◽  
pp. 503-508 ◽  
Author(s):  
Ardan Patwardhan
Keyword(s):  
Electron Microscopy ◽  
Three Dimensional ◽  
Data Bank ◽  
Electron Microscopy Data ◽  
Technological Advances ◽  
Major Player ◽  
Leading Position ◽  
Microscopy Data ◽  
The Uk ◽  
Better Than

Recent technological advances, such as the introduction of the direct electron detector, have transformed the field of cryo-EM and the landscape of molecular and cellular structural biology. This study analyses these trends from the vantage point of the Electron Microscopy Data Bank (EMDB), the public archive for three-dimensional EM reconstructions. Over 1000 entries were released in 2016, representing almost a quarter of the total number of entries (4431). Structures at better than 6 Å resolution now represent one of the fastest-growing categories, while the share of annually released tomography-related structures is approaching 20%. The use of direct electron detectors is growing very rapidly: they were used for 70% of the structures released in 2016, in contrast to none before 2011. Microscopes from FEI have an overwhelming lead in terms of usage, and the use of theRELIONsoftware package continues to grow rapidly after having attained a leading position in the field. China is rapidly emerging as a major player in the field, supplementing the US, Germany and the UK as the big four. Similarly, Tsinghua University ranks only second to the MRC Laboratory for Molecular Biology in terms of involvement in publications associated with cryo-EM structures at better than 4 Å resolution. Overall, the numbers point to a rapid democratization of the field, with more countries and institutes becoming involved.

scholarly journals Macromolecular X-ray crystallography: soon to be a road less travelled?

2020 ◽  
Vol 76 (5) ◽  
pp. 400-405 ◽  
Author(s):  
John H. Beale
Keyword(s):  
Electron Microscopy ◽  
Life Expectancy ◽  
Protein Data Bank ◽  
Structural Biology ◽  
Data Bank ◽  
New Labour ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy

The number of new X-ray crystallography-based submissions to the Protein Data Bank appears to be at the beginning of a decline, perhaps signalling an end to the era of the dominance of X-ray crystallography within structural biology. This letter, from the viewpoint of a young structural biologist, applies the Copernican method to the life expectancy of crystallography and asks whether the technique is still the mainstay of structural biology. A study of the rate of Protein Data Bank depositions allows a more nuanced analysis of the fortunes of macromolecular X-ray crystallography and shows that cryo-electron microscopy might now be outcompeting crystallography for new labour and talent, perhaps heralding a change in the landscape of the field.

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