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

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posted on 2012-10-24, 08:53 authored by J. F. Doreleijers, W. F. Vranken, C. Schulte, J. L. Markley, E. L. Ulrich, G. Vriend, G. W. Vuister
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.

History

Citation

Nucleic Acids Research, 2012, 40 (Database issue), pp. D519-D524

Version

  • VoR (Version of Record)

Published in

Nucleic Acids Research

Publisher

Oxford University Press

issn

0305-1048

eissn

1362-4962

Copyright date

2011

Available date

2012-10-24

Publisher version

http://nar.oxfordjournals.org/content/40/D1/D519

Language

eng

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