Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge

Terwilliger, Thomas C.; Adams, Paul D.; Afonine, Pavel V.; Sobolev, Oleg V.

doi:10.1016/j.jsb.2018.07.016

Title: Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge

Abstract

A recently-developed method for identifying a compact, contiguous region representing the unique part of a density map was applied to 218 Cryo-EM maps with resolutions of 4.5 Å or better. The key elements of the segmentation procedure are (1) identification of all regions of density above a threshold and (2) choice of a unique set of these regions, taking symmetry into consideration, that maximize connectivity and compactness. This segmentation approach was then combined with tools for automated map sharpening and model-building to generate models for the 12 maps in the 2016 Cryo-EM Model Challenge in a fully automated manner. The resulting models have completeness from 24% to 82% and RMS distances from reference interpretations of 0.6 Å-2.1 Å.

Authors:: Terwilliger, Thomas C.; Adams, Paul D.; Afonine, Pavel V.; Sobolev, Oleg V.

Publication Date:: Thu Nov 01 00:00:00 EDT 2018

Research Org.:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: National Institutes of Health (NIH); USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1463215

Alternate Identifier(s):: OSTI ID: 1467212; OSTI ID: 1974374

Report Number(s):: LA-UR-18-20543
Journal ID: ISSN 1047-8477; S104784771830193X; PII: S104784771830193X

Grant/Contract Number:: AC02-05CH11231; AC52-06NA25396; GM063210

Resource Type:: Published Article

Journal Name:: Journal of Structural Biology

Additional Journal Information:: Journal Name: Journal of Structural Biology Journal Volume: 204 Journal Issue: 2; Journal ID: ISSN 1047-8477

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Biological Science; Electron cryo-microscopy; Model-building; Map segmentation

Citation Formats


                    Terwilliger, Thomas C., Adams, Paul D., Afonine, Pavel V., and Sobolev, Oleg V. Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge.  United States: N. p., 2018. 
Web.  doi:10.1016/j.jsb.2018.07.016.

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                    Terwilliger, Thomas C., Adams, Paul D., Afonine, Pavel V., & Sobolev, Oleg V. Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge.  United States.  https://doi.org/10.1016/j.jsb.2018.07.016

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                    Terwilliger, Thomas C., Adams, Paul D., Afonine, Pavel V., and Sobolev, Oleg V. Thu .  
"Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge".  United States.  https://doi.org/10.1016/j.jsb.2018.07.016.

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@article{osti_1463215,

  title        = {Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge},

  author       = {Terwilliger, Thomas C. and Adams, Paul D. and Afonine, Pavel V. and Sobolev, Oleg V.},

  abstractNote = {A recently-developed method for identifying a compact, contiguous region representing the unique part of a density map was applied to 218 Cryo-EM maps with resolutions of 4.5 Å or better. The key elements of the segmentation procedure are (1) identification of all regions of density above a threshold and (2) choice of a unique set of these regions, taking symmetry into consideration, that maximize connectivity and compactness. This segmentation approach was then combined with tools for automated map sharpening and model-building to generate models for the 12 maps in the 2016 Cryo-EM Model Challenge in a fully automated manner. The resulting models have completeness from 24% to 82% and RMS distances from reference interpretations of 0.6 Å-2.1 Å.},

  doi          = {10.1016/j.jsb.2018.07.016},

  journal      = {Journal of Structural Biology},

  number       = 2,

  volume       = 204,

  place        = {United States},

  year         = {Thu Nov 01 00:00:00 EDT 2018},

  month        = {Thu Nov 01 00:00:00 EDT 2018}

}

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https://doi.org/10.1016/j.jsb.2018.07.016

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Cited by: 5 works

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Figures / Tables:

Fig. 1A: Segmentation of density for the anthrax protective antigen pore. A. Deposited structure of anthrax protective antigen pore with one of the 7 chains in purple. B. Density map illustrating the 7-fold symmetry used in the reconstruction. C. Individual segmented regions of the map superimposed on a single chainmore »

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Works referencing / citing this record:

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps
journal, October 2018

Terwilliger, Thomas C.; Adams, Paul D.; Afonine, Pavel V.
Nature Methods, Vol. 15, Issue 11
DOI: 10.1038/s41592-018-0173-1

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps
journal, October 2018

Terwilliger, Thomas C.; Adams, Paul D.; Afonine, Pavel V.
Nature Methods, Vol. 15, Issue 11
DOI: 10.1038/s41592-018-0173-1

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Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.

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Title: Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge

Abstract

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