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

Lawson, Catherine L.; Kryshtafovych, Andriy; Adams, Paul D.; Afonine, Pavel V.; Baker, Matthew L.; Barad, Benjamin A.; Bond, Paul; Burnley, Tom; Cao, Renzhi; Cheng, Jianlin; Chojnowski, Grzegorz; Cowtan, Kevin; Dill, Ken A.; DiMaio, Frank; Farrell, Daniel P.; Fraser, James S.; Herzik Jr., Mark A. Herzik; Hoh, Soon Wen; Hou, Jie; Hung, Li-Wei; Igaev, Maxim; Joseph, Agnel P.; Kihara, Daisuke; Kumar, Dilip; Mittal, Sumit; Monastyrskyy, Bohdan; Olek, Mateusz; Palmer, Colin M.; Patwardhan, Ardan; Perez, Alberto; Pfab, Jonas; Pintilie, Grigore D.; Richardson, Jane S.; Rosenthal, Peter B.; Sarkar, Daipayan; Schäfer, Luisa U.; Schmid, Michael F.; Schröder, Gunnar F.; Shekhar, Mrinal; Si, Dong; Singharoy, Abishek; Terashi, Genki; Terwilliger, Thomas C.; Vaiana, Andrea; Wang, Liguo; Wang, Zhe; Wankowicz, Stephanie A.; Williams, Christopher J.; Winn, Martyn; Wu, Tianqi; Yu, Xiaodi; Zhang, Kaiming; Berman, Helen M.; Chiu, Wah

doi:10.1038/s41592-020-01051-w

Local TagsRelease HistoryDetailsSummary

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

Lawson, C. L., Kryshtafovych, A., Adams, P. D., Afonine, P. V., Baker, M. L., Barad, B. A., et al. (2021). Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods, 18, 156-164. doi:10.1038/s41592-020-01051-w.

Item is Released

show all hide all

Basic

show hide

Item Permalink: https://hdl.handle.net/21.11116/0000-000B-3145-0 Version Permalink: https://hdl.handle.net/21.11116/0000-000B-50B6-D

Genre: Journal Article

Files

show Files

hide Files

:

s41592-020-01051-w.pdf (Publisher version), 7MB

View Save

File Permalink:
https://hdl.handle.net/21.11116/0000-000B-3147-E

Name:
s41592-020-01051-w.pdf

Description:
-

OA-Status:
Hybrid

Visibility:
Public

MIME-Type / Checksum:
application/pdf / [MD5]

Technical Metadata:

View

Copyright Date:
-

Copyright Info:
-

License:
http://creativecommons.org/licenses/by/4.0/

:

2020.06.12.147033v1.full.pdf (Preprint), 12MB

View Save

File Permalink:
https://hdl.handle.net/21.11116/0000-000B-3152-1

Name:
2020.06.12.147033v1.full.pdf

Description:
-

OA-Status:
Green

Visibility:
Public

MIME-Type / Checksum:
application/pdf / [MD5]

Technical Metadata:

View

Copyright Date:
-

Copyright Info:
-

License:
-

Locators

show

Creators

show

hide

Creators:
Lawson, Catherine L., Author
Kryshtafovych, Andriy, Author
Adams, Paul D., Author
Afonine, Pavel V., Author
Baker, Matthew L., Author
Barad, Benjamin A., Author
Bond, Paul, Author
Burnley, Tom, Author
Cao, Renzhi, Author
Cheng, Jianlin, Author
Chojnowski, Grzegorz, Author
Cowtan, Kevin, Author
Dill, Ken A., Author
DiMaio, Frank, Author
Farrell, Daniel P., Author
Fraser, James S., Author
Herzik Jr., Mark A. Herzik, Author
Hoh, Soon Wen, Author
Hou, Jie, Author
Hung, Li-Wei, Author
Igaev, Maxim¹, Author Joseph, Agnel P., AuthorKihara, Daisuke, AuthorKumar, Dilip, AuthorMittal, Sumit, AuthorMonastyrskyy, Bohdan, AuthorOlek, Mateusz, AuthorPalmer, Colin M., AuthorPatwardhan, Ardan, AuthorPerez, Alberto, AuthorPfab, Jonas, AuthorPintilie, Grigore D., AuthorRichardson, Jane S., AuthorRosenthal, Peter B., AuthorSarkar, Daipayan, AuthorSchäfer, Luisa U., AuthorSchmid, Michael F., AuthorSchröder, Gunnar F., AuthorShekhar, Mrinal, AuthorSi, Dong, AuthorSingharoy, Abishek, AuthorTerashi, Genki¹, AuthorTerwilliger, Thomas C., AuthorVaiana, Andrea¹, Author Wang, Liguo, AuthorWang, Zhe, AuthorWankowicz, Stephanie A., AuthorWilliams, Christopher J., AuthorWinn, Martyn, AuthorWu, Tianqi, AuthorYu, Xiaodi, AuthorZhang, Kaiming, AuthorBerman, Helen M., AuthorChiu, Wah, Author more..

Affiliations:
1Department of Theoretical and Computational Biophysics, MPI for Biophysical Chemistry, Max Planck Society, ou_578631

Content

show

hide

Free keywords: -

Abstract: 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.

Details

show

hide

Language(s): eng - English

Dates: Published Online: 2021-02-04

Publication Status: Published online

Pages: -

Publishing info: -

Table of Contents: -

Rev. Type: Peer

Identifiers: DOI: 10.1038/s41592-020-01051-w

Degree: -

Event

show

Legal Case

show

Project information

show hide

Project name : EMDataResource (C.L.L., A.K., G.P., H.M.B. and W.C.) is supported by the US National Institutes of Health (NIH)/National Institute of General Medical Science, grant no. R01GM079429. The Singharoy team used the supercomputing resources of the Oak Ridge Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science at the Department of Energy under contract no. DE-AC05-00OR22725. The following additional grants are acknowledged for participant support: grant no. NIH/R35GM131883 to J.S.R. and C.W.; grant no. NIH/P01GM063210 to P.D.A., P.V.A., L.-W.H., J.S.R., T.C.T. and C.W.; National Science Foundation grant no. (NSF)/MCB-1942763 (CAREER) and NIH/R01GM095583 to A.S.; grant nos. NIH/R01GM123055, NIH/R01GM133840, NSF/DMS1614777, NSF/CMMI1825941, NSF/MCB1925643, NSF/DBI2003635 and Purdue Institute of Drug Discovery to D. Kihara; grant no. NIH/R01GM123159 to J.S.F.; Max Planck Society German Research Foundation grant no. IG 109/1-1 to M.I.; Max Planck Society German Research Foundation grant no. FOR-1805 to A.C.V.; grant nos. NIH/R37AI36040 and Welch Foundation/Q1279 to D. Kumar (PI: BVV Prasad); grant no. NSF/DBI2030381 to D. Si.; Medical Research Council grant no. MR/N009614/1 to T.B., C.M.P. and M.W.; Wellcome Trust grant no. 208398/Z/17/Z to A.P.J. and M.W.; Biotechnology and Biological Sciences Research Council grant no. BB/P000517/1 to K.C. and Biotechnology and Biological Sciences Research Council grant no. BB/P000975/1 to M.W.

Grant ID : -

Funding program : -

Funding organization : -

Source 1

show

hide

Title: Nature Methods

Other : Nature Methods

Source Genre: Journal

Creator(s):

Affiliations:

Publ. Info: New York, NY : Nature Publishing Group

Pages: - Volume / Issue: 18 Sequence Number: - Start / End Page: 156 - 164 Identifier: ISSN: 1548-7091
CoNE: https://pure.mpg.de/cone/journals/resource/111088195279556