Format

Send to

Choose Destination
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.

Author information

1
Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA. Electronic address: akryshtafovych@ucdavis.edu.
2
Molecular Biophysics & Integrated Bioimaging, LBNL, CA 94720, USA; Department of Bioengineering, University of California Berkeley, CA 94720, USA.
3
Institute for Quantitative Biomedicine and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA.
4
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.

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

Supplemental Content

Full text links

Icon for Elsevier Science Icon for PubMed Central
Loading ...
Support Center