ArticleNucleic acids research2012
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.Structure (London, England : 1993) · 2024Article
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- Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.Methods in molecular biology (Clifton, N.J.) · 2017Review
- Resolution ofIUCrJ · 2016Article
- Analysis of the structural quality of the CASD-NMR 2013 entries.Journal of biomolecular NMR · 2015Article
- Structural insights into and activity analysis of the antimicrobial peptide myxinidin.Antimicrobial agents and chemotherapy · 2014Article
- Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta.Journal of biomolecular NMR · 2014Article
- Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1.Nucleic acids research · 2014Article
- An overview of tools for the validation of protein NMR structures.Journal of biomolecular NMR · 2014Review
- The structure, stability and pheromone binding of the male mouse protein sex pheromone darcin.PloS one · 2014Article
- Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement.Acta crystallographica. Section D, Biological crystallography · 2013Article
- Quality assessment of protein NMR structures.Current opinion in structural biology · 2013Review
- PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.Journal of biomolecular NMR · 2013Article
- The role of structural bioinformatics resources in the era of integrative structural biology.Acta crystallographica. Section D, Biological crystallography · 2013Article
- Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.Proteins · 2013Article
- An assignment of intrinsically disordered regions of proteins based on NMR structures.Journal of structural biology · 2013Article
- CING: an integrated residue-based structure validation program suite.Journal of biomolecular NMR · 2012Article
- The structure of myristoylated Mason-Pfizer monkey virus matrix protein and the role of phosphatidylinositol-(4,5)-bisphosphate in its membrane binding.Journal of molecular biology · 2012Article
- The apo-structure of the low molecular weight protein-tyrosine phosphatase A (MptpA) from Mycobacterium tuberculosis allows for better target-specific drug development.The Journal of biological chemistry · 2012Article
- NMR and crystal structures of the Pyrococcus horikoshii RadA intein guide a strategy for engineering a highly efficient and promiscuous intein.Journal of molecular biology · 2012Article
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7 authors.
Funding
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.
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