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.Electronic supplementary materialThe online version of this article (doi:10.1007/s10858-015-9953-4) contains supplementary material, which is available to authorized users.
Highlights
Manual determination of a protein structure from nuclear magnetic resonance (NMR) spectroscopy data is a timeconsuming process, taking weeks up to several months for unfavorable cases
Two sets of NOE spectroscopy (NOESY) peak list data were provided for each protein target in CASD-NMR-2013: (1) initial automatically-picked un-curated NOESY peak lists and (2) the final manually-curated NOESY peak lists used for generating the reference structures that are deposited in the PDB
The results of CASD-NMR-2013 provide a comprehensive comparison of the performance of most currently available programs for automated protein structure generation from NMR data
Summary
Manual determination of a protein structure from nuclear magnetic resonance (NMR) spectroscopy data is a timeconsuming process, taking weeks up to several months for unfavorable cases. 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.
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