Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge
Abstract
142 protein structure models were submitted to second Cryo-EM model challenge (2015-2016). Accuracy of the models was evaluated with 54 evaluation scores. Results of the descriptive statistical analysis of the scores are provided in this article.
- Authors:
-
[1];
- Univ. of California, Davis, CA (United States). Genome Center
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics & Integrated Bioimaging; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
- Rutgers Univ., Piscataway, NJ (United States). Inst. for Quantitative Biomedicine and Research Collaboratory for Structural Bioinformatics
- Stanford Univ., CA (United States). Dept. of Bioengineering, Microbiology and Immunology and Photon Science
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1560562
- Grant/Contract Number:
- AC02-05CH11231; R01GM079429; P01GM063210
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Data in Brief
- Additional Journal Information:
- Journal Volume: 20; Journal Issue: C; Journal ID: ISSN 2352-3409
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Kryshtafovych, Andriy, Monastyrskyy, Bohdan, Adams, Paul D., Lawson, Catherine L., and Chiu, Wah. Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge. United States: N. p., 2018.
Web. doi:10.1016/j.dib.2018.08.214.
Kryshtafovych, Andriy, Monastyrskyy, Bohdan, Adams, Paul D., Lawson, Catherine L., & Chiu, Wah. Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge. United States. https://doi.org/10.1016/j.dib.2018.08.214
Kryshtafovych, Andriy, Monastyrskyy, Bohdan, Adams, Paul D., Lawson, Catherine L., and Chiu, Wah. Sat .
"Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge". United States. https://doi.org/10.1016/j.dib.2018.08.214. https://www.osti.gov/servlets/purl/1560562.
@article{osti_1560562,
title = {Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge},
author = {Kryshtafovych, Andriy and Monastyrskyy, Bohdan and Adams, Paul D. and Lawson, Catherine L. and Chiu, Wah},
abstractNote = {142 protein structure models were submitted to second Cryo-EM model challenge (2015-2016). Accuracy of the models was evaluated with 54 evaluation scores. Results of the descriptive statistical analysis of the scores are provided in this article.},
doi = {10.1016/j.dib.2018.08.214},
journal = {Data in Brief},
number = C,
volume = 20,
place = {United States},
year = {Sat Sep 08 00:00:00 EDT 2018},
month = {Sat Sep 08 00:00:00 EDT 2018}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Critical assessment of methods of protein structure prediction (CASP)-Round XII
journal, December 2017
- Moult, John; Fidelis, Krzysztof; Kryshtafovych, Andriy
- Proteins: Structure, Function, and Bioinformatics, Vol. 86
Evaluation system and web infrastructure for the second cryo-EM model challenge
journal, October 2018
- Kryshtafovych, Andriy; Adams, Paul D.; Lawson, Catherine L.
- Journal of Structural Biology, Vol. 204, Issue 1
MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009
- Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
journal, November 2002
- Zhou, Hongyi; Zhou, Yaoqi
- Protein Science, Vol. 11, Issue 11
ProQ3: Improved model quality assessments using Rosetta energy terms
journal, October 2016
- Uziela, Karolis; Shu, Nanjiang; Wallner, Björn
- Scientific Reports, Vol. 6, Issue 1
QMEAN server for protein model quality estimation
journal, May 2009
- Benkert, Pascal; Künzli, Michael; Schwede, Torsten
- Nucleic Acids Research, Vol. 37, Issue suppl_2
LGA: a method for finding 3D similarities in protein structures
journal, July 2003
- Zemla, A.
- Nucleic Acids Research, Vol. 31, Issue 13
TM-align: a protein structure alignment algorithm based on the TM-score
journal, April 2005
- Zhang, Y.
- Nucleic Acids Research, Vol. 33, Issue 7
Scoring function for automated assessment of protein structure template quality
journal, January 2004
- Zhang, Yang; Skolnick, Jeffrey
- Proteins: Structure, Function, and Bioinformatics, Vol. 57, Issue 4
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
journal, August 2013
- Mariani, Valerio; Biasini, Marco; Barbato, Alessandro
- Bioinformatics, Vol. 29, Issue 21
CAD-score: A new contact area difference-based function for evaluation of protein structural models
journal, September 2012
- Olechnovič, Kliment; Kulberkytė, Eleonora; Venclovas, Česlovas
- Proteins: Structure, Function, and Bioinformatics, Vol. 81, Issue 1
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology
journal, September 2017
- Bertoni, Martino; Kiefer, Florian; Biasini, Marco
- Scientific Reports, Vol. 7, Issue 1
Assessment of protein assembly prediction in CASP12
journal, November 2017
- Lafita, Aleix; Bliven, Spencer; Kryshtafovych, Andriy
- Proteins: Structure, Function, and Bioinformatics, Vol. 86
Scoring functions for cryoEM density fitting
journal, May 2011
- Vasishtan, Daven; Topf, Maya
- Journal of Structural Biology, Vol. 174, Issue 2
TEMPy : a Python library for assessment of three-dimensional electron microscopy density fits
journal, June 2015
- Farabella, Irene; Vasishtan, Daven; Joseph, Agnel Praveen
- Journal of Applied Crystallography, Vol. 48, Issue 4
EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
journal, August 2015
- Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei
- Nature Methods, Vol. 12, Issue 10
CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL: CASP Prediction Center
journal, October 2013
- Kryshtafovych, Andriy; Monastyrskyy, Bohdan; Fidelis, Krzysztof
- Proteins: Structure, Function, and Bioinformatics, Vol. 82
Works referencing / citing this record:
Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results
journal, August 2019
- Kryshtafovych, Andriy; Malhotra, Sony; Monastyrskyy, Bohdan
- Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 12