NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.

TitleNRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.
Publication TypeJournal Article
Year of Publication2012
AuthorsDoreleijers, J. F., W. F. Vranken, C. Schulte, J. L. Markley, E. L. Ulrich, G. Vriend, and G. W. Vuister
JournalNucleic Acids Res
Volume40
IssueDatabase issue
PaginationD519-24
Date Published2012 Jan
ISSN1362-4962
KeywordsDatabases, Protein, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation, Reproducibility of Results, Systems Integration
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.

DOI10.1093/nar/gkr1134
Alternate JournalNucleic Acids Res.
PubMed ID22139937
PubMed Central IDPMC3245154
Grant ListBB/J007897/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
LM05799 / LM / NLM NIH HHS / United States
P41 LM005799 / LM / NLM NIH HHS / United States
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