3D-Strudel - a novel model-dependent map-feature validation method for high-resolution cryo-EM structures

Recent technological advances in electron cryo-microscopy (cryo-EM) have led to significant improvements in the resolution of many single-particle reconstructions and a sharp increase in the number of entries released in the Electron Microscopy Data Bank (EMDB) every year, which in turn has opened new possibilities for data mining. Here we present a resolution-dependent library of rotamer-specific amino-acid map motifs mined from entries in the EMDB archive with reported resolution between 2.0 and 4.0A. We further describe 3D-Strudel, a method for map/model validation based on these libraries. 3D-Strudel calculates linear correlation coefficients between the map values of a map-motif from the library and the experimental map values around a target residue. We also present "Strudel Score", a plug-in for ChimeraX, as a user-friendly tool for visualisation of 3D-Strudel validation results.

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Trends in the Electron Microscopy Data Bank (EMDB)

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798317004181 ◽

2017 ◽

Vol 73 (6) ◽

pp. 503-508 ◽

Cited By ~ 43

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.

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VASEM: visual analytics system for electron microscopy data bank

Journal of Visualization ◽

10.1007/s12650-019-00597-y ◽

2019 ◽

Vol 22 (6) ◽

pp. 1145-1159 ◽

Cited By ~ 1

Author(s):

Jun Liu ◽

Yang Gao ◽

Guihua Shan ◽

Xuebin Chi

Keyword(s):

Electron Microscopy ◽

Visual Analytics ◽

Data Bank ◽

Electron Microscopy Data ◽

Microscopy Data

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

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798318009324 ◽

2018 ◽

Vol 74 (9) ◽

pp. 814-840 ◽

Cited By ~ 183

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.

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A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data

The Bacterial Nucleoid - Methods in Molecular Biology ◽

10.1007/978-1-4939-7098-8_15 ◽

2017 ◽

pp. 193-210

Author(s):

Damien Larivière ◽

Rodrigo Galindo-Murillo ◽

Eric Fourmentin ◽

Samuel Hornus ◽

Bruno Lévy ◽

...

Keyword(s):

Electron Microscopy ◽

Cryo Electron Microscopy ◽

Electron Microscopy Data ◽

Modeling Software ◽

Dna Modeling ◽

Microscopy Data ◽

User Friendly

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

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314085210 ◽

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.

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

10.1101/279844 ◽

2018 ◽

Cited By ~ 5

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.

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