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

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. As a result, 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.

Authors:
ORCiD logo [1];  [2];  [3];  [4]
  1. Univ. of California, Davis, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
  3. The State Univ. of New Jersey, Piscataway, NJ (United States)
  4. Stanford Univ., Stanford, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1490827
Grant/Contract Number:  
AC02-76SF00515
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Structural Biology
Additional Journal Information:
Journal Volume: 204; Journal Issue: 1; Journal ID: ISSN 1047-8477
Publisher:
Elseiver
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Cryo-EM; Model challenge; Protein structure modeling; Protein structure verification

Citation Formats

Kryshtafovych, Andriy, Adams, Paul D., Lawson, Catherine L., and Chiu, Wah. Evaluation system and web infrastructure for the second cryo-EM model challenge. United States: N. p., 2018. Web. doi:10.1016/j.jsb.2018.07.006.
Kryshtafovych, Andriy, Adams, Paul D., Lawson, Catherine L., & Chiu, Wah. Evaluation system and web infrastructure for the second cryo-EM model challenge. United States. doi:10.1016/j.jsb.2018.07.006.
Kryshtafovych, Andriy, Adams, Paul D., Lawson, Catherine L., and Chiu, Wah. Thu . "Evaluation system and web infrastructure for the second cryo-EM model challenge". United States. doi:10.1016/j.jsb.2018.07.006. https://www.osti.gov/servlets/purl/1490827.
@article{osti_1490827,
title = {Evaluation system and web infrastructure for the second cryo-EM model challenge},
author = {Kryshtafovych, Andriy and Adams, Paul D. and Lawson, Catherine L. and Chiu, Wah},
abstractNote = {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. As a result, 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.},
doi = {10.1016/j.jsb.2018.07.006},
journal = {Journal of Structural Biology},
number = 1,
volume = 204,
place = {United States},
year = {2018},
month = {7}
}

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