TY - JOUR
T1 - Evaluation system and web infrastructure for the second cryo-EM model challenge
AU - Kryshtafovych, Andriy
AU - Adams, Paul D.
AU - Lawson, Catherine L.
AU - Chiu, Wah
N1 - Funding Information: We are grateful to Pavel Afonine and Tom Terwilliger (PHENIX), Benjamin Barad (EMRinger), Maya Topf and Agnel P. Joseph (TEMPy) for providing their software for the cryo-EM model challenge evaluation, for the help in adjusting the software to the needs of the EMMC evaluation and for discussing details of their tools. Big thanks go to Bohdan Monastyrskyy (UC Davis) and Kenneth Dalenberg (Rutgers) for their help with setting up the web server. Authors acknowledge support of the National Institute of General Medical Sciences grant R01GM079429 to WC, and grant P01GM063210 to PDA. Publisher Copyright: © 2018 Elsevier Inc.
PY - 2018/10
Y1 - 2018/10
N2 - 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.
AB - 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.
KW - Cryo-EM
KW - Model challenge
KW - Protein structure modeling
KW - Protein structure verification
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U2 - https://doi.org/10.1016/j.jsb.2018.07.006
DO - https://doi.org/10.1016/j.jsb.2018.07.006
M3 - Article
C2 - 30017700
SN - 1047-8477
VL - 204
SP - 96
EP - 108
JO - Journal of Structural Biology
JF - Journal of Structural Biology
IS - 1
ER -