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Creator: Doreleijers, Jurgen F.; et al.
Publisher: Radboud Universiteit Nijmegen
Abstract: NRG-CING is created using code in CING. Please visit this website for more information on CING. The NRG-CING website is a collection of CING reports that has been pre-calculated for all PDB files solved by NMR. In case the underlying experimental data is available, these have been cleaned up and made syntactically and semantically correct and homogeneous. This webserver is described in: NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB, J.F. Doreleijers, W.F. Vranken, C. Schulte, J.L. Markley, E.L. Ulrich, G. Vriend, and G. W. Vuister. For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists used in the structure calculation are accessible, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. Assessment of the quality of the structural result is paramount to their usage and a combined, integrated repository of both input data and structural results greatly facilitates such an analysis. In addition, the accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculations using the available experimental data and present-day software with improved protocols and force fields. Such efforts, however, generally fail on over half of all deposited structures due to the syntactic and semantic heterogeneity of the data and the wide variety of formats used for their deposition. We have combined the cleaned-up restraints information from the NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank in the weekly updated NRG-CING database. Eleven programs, in addition to CING itself, 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 restraint and chemical shift data. The longitudinal validation of this data yielded a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The cleaned up NMR experimental datasets and the validation reports are freely available. [Information of the supplier]
Subject: Proteins (572.6)
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Audience: Experts
Language: English
Format: website; database
Resource type: Factual databases
Access: free
Metadata update date: 2015-06-12
Metadata provider: UBFfm
URL of this vifabio-resource:
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