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

Catherine L. Lawson(Rutgers, The State University of New Jersey), Andriy Kryshtafovych(University of California, Davis), Paul D. Adams(Lawrence Berkeley National Laboratory), Pavel V. Afonine(Lawrence Berkeley National Laboratory), Matthew L. Baker(The University of Texas Health Science Center at Houston), Benjamin A. Barad(Scripps Research Institute), Paul S. Bond(University of York), Tom Burnley(Science and Technology Facilities Council), Renzhi Cao(Pacific Lutheran University), Jianlin Cheng(University of Missouri), Grzegorz Chojnowski(European Molecular Biology Laboratory), Kevin Cowtan(University of York), Ken A. Dill(Stony Brook University), Frank DiMaio(University of Washington), Daniel P. Farrell(University of Washington), James S. Fraser(University of California, San Francisco), Mark A. Herzik(University of California San Diego), Soon Wen Hoh(University of York), Jie Hou(Saint Louis University), Li‐Wei Hung(Los Alamos National Laboratory), Maxim Igaev(Max Planck Institute for Biophysical Chemistry), Agnel Praveen Joseph(Science and Technology Facilities Council), Daisuke Kihara(Purdue University West Lafayette), Dilip Kumar(Baylor College of Medicine), Sumit Mittal(Barkatullah University), Bohdan Monastyrskyy(University of California, Davis), Mateusz Olek(University of York), Colin M. Palmer(Science and Technology Facilities Council), Ardan Patwardhan(European Bioinformatics Institute), Alberto Pérez(University of Florida), Jonas Pfab(University of Washington Bothell), Grigore Pintilie(Stanford University), Jane S. Richardson(Duke University), Peter B. Rosenthal(The Francis Crick Institute), Daipayan Sarkar(Purdue University West Lafayette), Luisa U. Schäfer(Forschungszentrum Jülich), Michael F. Schmid(SLAC National Accelerator Laboratory), Gunnar F. Schröder(Forschungszentrum Jülich), Mrinal Shekhar(Broad Institute), Dong Si(University of Washington Bothell), Abishek Singharoy(Arizona State University), Genki Terashi(Max Planck Institute for Biophysical Chemistry), Thomas C. Terwilliger(New Mexico Consortium), Andrea C. Vaiana(Max Planck Institute for Biophysical Chemistry), Liguo Wang(University of Washington), Zhe Wang(European Bioinformatics Institute), Stephanie A. Wankowicz(University of California, San Francisco), Christopher J. Williams(Duke University), Martyn Winn(Science and Technology Facilities Council), Tianqi Wu(University of Missouri), Xiaodi Yu(Janssen (United States)), Kaiming Zhang(Stanford University), Helen M. Berman(Rutgers, The State University of New Jersey), Wah Chiu(SLAC National Accelerator Laboratory)
Nature Methods
February 1, 2021
10.1038/s41592-020-01051-w
Cited by 119Open Access
Full Text

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.

Related Papers

No related papers found

Powered by citation graph analysis