ArticleProteins2010
Validation of archived chemical shifts through atomic coordinates.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 39 citations in OpenAlex.
- Data-driven probabilistic definition of the low energy conformational states of protein residues.NAR genomics and bioinformatics · 2024Article
- ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values.Nucleic acids research · 2020Article
- Auto-encoding NMR chemical shifts from their native vector space to a residue-level biophysical index.Nature communications · 2019Article
- 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
- Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra.Nature communications · 2018Article
- Probabilistic validation of protein NMR chemical shift assignments.Journal of biomolecular NMR · 2016Article
- Analysis of the structural quality of the CASD-NMR 2013 entries.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
- PDBe: Protein Data Bank in Europe.Nucleic acids research · 2014Article
- 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
- Improving 3D structure prediction from chemical shift data.Journal of biomolecular NMR · 2013Article
- Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.Proteins · 2013Article
- NightShift: NMR shift inference by general hybrid model training--a framework for NMR chemical shift prediction.BMC bioinformatics · 2013Article
- CING: an integrated residue-based structure validation program suite.Journal of biomolecular NMR · 2012Article
- PDBe: Protein Data Bank in Europe.Nucleic acids research · 2012Article
- NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.Nucleic acids research · 2012Article
- Structure-based prediction of methyl chemical shifts in proteins.Journal of biomolecular NMR · 2011Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
The public archives containing protein information in the form of NMR chemical shift data at the BioMagResBank (BMRB) and of 3D structure coordinates at the Protein Data Bank are continuously expanding. The quality of the data contained in these archives, however, varies. The main issue for chemical shift values is that they are determined relative to a reference frequency. When this reference frequency is set incorrectly, all related chemical shift values are systematically offset. Such wrongly referenced chemical shift values, as well as other problems such as chemical shift values that are assigned to the wrong atom, are not easily distinguished from correct values and effectively reduce the usefulness of the archive. We describe a new method to correct and validate protein chemical shift values in relation to their 3D structure coordinates. This method classifies atoms using two parameters: the per-atom solvent accessible surface area (as calculated from the coordinates) and the secondary structure of the parent amino acid. Through the use of Gaussian statistics based on a large database of 3220 BMRB entries, we obtain per-entry chemical shift corrections as well as Z scores for the individual chemical shift values. In addition, information on the error of the correction value itself is available, and the method can retain only dependable correction values. We provide an online resource with chemical shift, atom exposure, and secondary structure information for all relevant BMRB entries (http://www.ebi.ac.uk/pdbe/nmr/vasco) and hope this data will aid the development of new chemical shift-based methods in NMR.
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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.