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

  • Author(s): 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, Mark A;
  • 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
  • et al.
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.

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