Please use this identifier to cite or link to this item: http://hdl.handle.net/2381/32412
Title: The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013
Authors: Rosato, A.
Vranken, W
Fogh, Rasmus H.
Ragan, Timothy J.
Tejero, R.
Pederson, K.
Lee, H. W.
Prestegard, J. H.
Yee, A.
Wu, B.
Lemak, A.
Houliston, S.
Arrowsmith, C. H.
Kennedy, M.
Acton, T. B.
Xiao, R.
Liu, G.
Montelione, G. T.
Vuister, Geerten W.
First Published: 14-Jun-2015
Publisher: Springer Netherlands
Citation: Journal of Biomolecular NMR, 2015
Abstract: The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100 % of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90 % of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.
DOI Link: 10.1007/s10858-015-9953-4
ISSN: 0925-2738
eISSN: 1573-5001
Links: http://link.springer.com/article/10.1007%2Fs10858-015-9953-4#
http://hdl.handle.net/2381/32412
Version: Publisher Version
Status: Peer-reviewed
Type: Journal Article
Rights: Copyright © the authors, 2015. This is an open-access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/ ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Appears in Collections:Published Articles, Dept. of Biochemistry

Files in This Item:
File Description SizeFormat 
art%3A10.1007%2Fs10858-015-9953-4.pdfPublished (publisher PDF)1.02 MBAdobe PDFView/Open


Items in LRA are protected by copyright, with all rights reserved, unless otherwise indicated.