ArticleBMC structural biology2009
Relationship between chemical shift value and accessible surface area for all amino acid atoms.
Article in BMC structural biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Accurate conformational ensembles of intrinsically disordered proteins using reweighting based on NMR chemical shifts.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- EFG-CS: Predicting chemical shifts from amino acid sequences with protein structure prediction using machine learning and deep learning models.Protein science : a publication of the Protein Society · 2024Article
- Comparative analysis ofJournal of biomolecular NMR · 2021Article
- Accurate prediction of chemical shifts for aqueous protein structure on "Real World" data.Chemical science · 2020Article
- Auto-encoding NMR chemical shifts from their native vector space to a residue-level biophysical index.Nature communications · 2019Article
- Rapid and reliable protein structure determination via chemical shift threading.Journal of biomolecular NMR · 2018Article
- Probabilistic validation of protein NMR chemical shift assignments.Journal of biomolecular NMR · 2016Article
- Article
- NMRFAM-SDF: a protein structure determination framework.Journal of biomolecular NMR · 2015Article
- Accessible surface area from NMR chemical shifts.Journal of biomolecular NMR · 2015Article
- Improving 3D structure prediction from chemical shift data.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
- Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field.Progress in nuclear magnetic resonance spectroscopy · 2012Review
- Loss of T cell antigen recognition arising from changes in peptide and major histocompatibility complex protein flexibility: implications for vaccine design.The Journal of biological chemistry · 2011Article
- Structure-based prediction of methyl chemical shifts in proteins.Journal of biomolecular NMR · 2011Article
- SHIFTX2: significantly improved protein chemical shift prediction.Journal of biomolecular NMR · 2011Article
- The Protein Data Bank in Europe (PDBe): bringing structure to biology.Acta crystallographica. Section D, Biological crystallography · 2011Article
- Straightforward and complete deposition of NMR data to the PDBe.Journal of biomolecular NMR · 2010Article
- Article
- PDBe: Protein Data Bank in Europe.Nucleic acids research · 2010Article
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Authors and funding
2 authors.
Funding
Abstract
backgroundChemical shifts obtained from NMR experiments are an important tool in determining secondary, even tertiary, protein structure. The main repository for chemical shift data is the BioMagResBank, which provides NMR-STAR files with this type of information. However, it is not trivial to link this information to available coordinate data from the PDB for non-backbone atoms due to atom and chain naming differences, as well as sequence numbering changes.
resultsWe here describe the analysis of a consistent set of chemical shift and coordinate data, in which we focus on the relationship between the per-atom solvent accessible surface area (ASA) in the reported coordinates and their reported chemical shift value. The data is available online on http://www.ebi.ac.uk/pdbe/docs/NMR/shiftAnalysis/index.html.
conclusionAtoms with zero per-atom ASA have a significantly larger chemical shift dispersion and often have a different chemical shift distribution compared to those that are solvent accessible. With higher per-atom ASA, the chemical shift values also tend towards random coil values. The per-atom ASA, although not the determinant of the chemical shift, thus provides a way to directly correlate chemical shift information to the atomic coordinates.
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