ArticleJournal of biomolecular NMR2010
A probabilistic approach for validating protein NMR chemical shift assignments.
Article in Journal of biomolecular NMR, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Complete NMR assignment for 275 of the most common dipeptides in intrinsically disordered proteins.Scientific data · 2026Article
- Solution NMR backbone assignment of the N-terminal tandem Zα1-Zα2 domains of Z-DNA binding protein 1.Biomolecular NMR assignments · 2024Article
- Rapid Quantification of Protein Secondary Structure Composition from a Single Unassigned 1DJournal of the American Chemical Society · 2024Article
- Accurate prediction of chemical shifts for aqueous protein structure on "Real World" data.Chemical science · 2020Article
- AutomaticJournal of biomolecular NMR · 2018Article
- Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra.Journal of biomolecular NMR · 2018Article
- Validation of Structures in the Protein Data Bank.Structure (London, England : 1993) · 2017Article
- Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling.Journal of the American Chemical Society · 2016Article
- NMRFx Processor: a cross-platform NMR data processing program.Journal of biomolecular NMR · 2016Article
- Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria.Journal of biomolecular NMR · 2016Article
- Probabilistic validation of protein NMR chemical shift assignments.Journal of biomolecular NMR · 2016Article
- Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression.Journal of biomolecular NMR · 2015Article
- NMRFAM-SDF: a protein structure determination framework.Journal of biomolecular NMR · 2015Article
- An overview of tools for the validation of protein NMR structures.Journal of biomolecular NMR · 2014Review
- Quality assessment of protein NMR structures.Current opinion in structural biology · 2013Review
- Recommendations of the wwPDB NMR Validation Task Force.Structure (London, England : 1993) · 2013Article
- Modeling proteins using a super-secondary structure library and NMR chemical shift information.Structure (London, England : 1993) · 2013Article
- NightShift: NMR shift inference by general hybrid model training--a framework for NMR chemical shift prediction.BMC bioinformatics · 2013Article
- Highly efficient NMR assignment of intrinsically disordered proteins: application to B- and T cell receptor domains.PloS one · 2013Article
- An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database.Journal of biomolecular NMR · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. The protocol described here has been implemented into a freely available Java program called "Probabilistic Approach for protein Nmr Assignment Validation (PANAV)" and as a web server ( http://redpoll.pharmacy.ualberta.ca/PANAV ) which can be used to validate and/or correct as well as re-reference assigned protein chemical shifts.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.