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

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

Abstract

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 http://model-compare.emdatabank.org.

Keywords: Cryo-EM; Model challenge; Protein structure modeling; Protein structure verification.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Cryoelectron Microscopy / methods*
  • Models, Molecular
  • Protein Conformation
  • Proteins / ultrastructure*

Substances

  • Proteins