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J Struct Biol. 2018 Oct;204(1):96-108. doi: 10.1016/j.jsb.2018.07.006. Epub 2018 Jul 12.

Evaluation system and web infrastructure for the second cryo-EM model challenge.

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Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA. Electronic address:
Molecular Biophysics & Integrated Bioimaging, LBNL, CA 94720, USA; Department of Bioengineering, University of California Berkeley, CA 94720, USA.
Institute for Quantitative Biomedicine and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA.
Departments of Bioengineering and Microbiology & Immunology, Stanford University, Stanford, CA 94305-5447, USA; Division of CryoEM and Bioimaging, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.


An evaluation system and a web infrastructure were developed for the second cryo-EM model challenge. The evaluation system includes tools to validate stereo-chemical plausibility of submitted models, check their fit to the corresponding density maps, estimate their overall and per-residue accuracy, and assess their similarity to reference cryo-EM or X-ray structures as well as other models submitted in this challenge. The web infrastructure provides a convenient interface for analyzing models at different levels of detail. It includes interactively sortable tables of evaluation scores for different subsets of models and different sublevels of structure organization, and a suite of visualization tools facilitating model analysis. The results are publicly accessible at


Cryo-EM; Model challenge; Protein structure modeling; Protein structure verification

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