Comparing cryo-EM structures

Lawson, Catherine L.; Chiu, Wah

doi:10.1016/j.jsb.2018.10.004

Cited by 31 publications

(34 citation statements)

References 36 publications

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“…CASP infrastructure for running the evaluation, reporting scores, and visualizing evaluation results for cryo‐EM targets (http://predictioncenter.org/casp13/cryoem_results.cgi) is based on the prototype of the evaluation infrastructure developed for the cryo‐EM model challenge …”

Section: Methodsmentioning

confidence: 99%

Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results

et al. 2019

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Structures of seven CASP13 targets were determined using cryo‐electron microscopy (cryo‐EM) technique with resolution between 3.0 and 4.0 Å. We provide an overview of the experimentally derived structures and describe results of the numerical evaluation of the submitted models. The evaluation is carried out by comparing coordinates of models to those of reference structures (CASP‐style evaluation), as well as checking goodness‐of‐fit of modeled structures to the cryo‐EM density maps. The performance of contributing research groups in the CASP‐style evaluation is measured in terms of backbone accuracy, all‐atom local geometry and similarity of inter‐subunit interfaces. The results on the cryo‐EM targets are compared with those on the whole set of eighty CASP13 targets. A posteriori refinement of the best models in their corresponding cryo‐EM density maps resulted in structures that are very close to the reference structure, including some regions with better fit to the density.

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Section: Methodsmentioning

confidence: 99%

Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results

et al. 2019

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“…Challenge process and organization. Informed by previous challenges 2,6,11 , the 2019 Model Challenge process was substantially streamlined in this round. In March, a panel of advisors with expertise in cryo-EM methods, modeling and/or model assessment was recruited.…”

Section: Methodsmentioning

confidence: 99%

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

et al. 2021

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This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

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“…The EMDR project website [ Fig. 5(a)] serves as a global resource for cryo-EM structure data and EM-related news, events, software tools, data standards, validation methods and community challenges (Lawson et al, 2016;Lawson & Chiu, 2018). The site also offers growth statistics for 3DEM structures in the PDB and maps in the EMDB [ Fig.…”

Section: Other Structural Biology Databasesmentioning

confidence: 99%

The data universe of structural biology

Berman

Vallat

Lawson

2020

IUCrJ

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The Protein Data Bank (PDB) has grown from a small data resource for crystallographers to a worldwide resource serving structural biology. The history of the growth of the PDB and the role that the community has played in developing standards and policies are described. This article also illustrates how other biophysics communities are collaborating with the worldwide PDB to create a network of interoperating data resources. This network will expand the capabilities of structural biology and enable the determination and archiving of increasingly complex structures.

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Comparing cryo-EM structures

Cited by 31 publications

References 36 publications

Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results

Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

The data universe of structural biology

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