Please use this identifier to cite or link to this item: http://hdl.handle.net/2381/26713
Title: NRG-CING: Integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB
Authors: Vuister, Geerten W.
Doreleijers, J. F.
Vriend, G.
Vranken, W. F.
Schulte, C.
Markley, J. L.
Ulrich, E. L.
First Published: Jan-2012
Publisher: Oxford University Press
Citation: Nucleic Acids Research, 2012, 40 (D1)
Abstract: For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists are available, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. The accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculation using the available experimental data and present-day software. Such efforts, however, generally fail on half of all NMR ensembles due to the syntactic and semantic heterogeneity of the underlying data and the wide variety of formats used for their deposition. We have combined the remediated restraint information from our NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank and the Common Interface for NMR structure Generation (CING) structure validation reports into the weekly updated NRG-CING database (http://nmr.cmbi.ru.nl/NRG-CING). Eleven programs have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available experimental NMR data. The longitudinal validation of these data in a publicly available relational database yields a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The remediated NMR experimental data sets and validation reports are freely available online.
DOI Link: 10.1093/nar/gkr1134
ISSN: 0305-1048
eISSN: 1362-4962
Links: http://hdl.handle.net/2381/26713
http://nar.oxfordjournals.org/content/40/D1/D519
Version: Publisher Version
Status: Peer-reviewed
Type: Journal Article
Rights: Copyright © The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Appears in Collections:Published Articles, Dept. of Biochemistry

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