ArticleJournal of biomolecular NMR2003
RefDB: a database of uniformly referenced protein chemical shifts.
Article in Journal of biomolecular NMR, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 224 papers.
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Who cites it
224 citing papers in PubMed.
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- Very broad distribution of β sheet registries of the HIV gp41 fusion peptide supports mutational robustness for fusion and infection.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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- UCBShift 2.0: Bridging the Gap from Backbone to Side Chain Protein Chemical Shift Prediction for Protein Structures.Journal of the American Chemical Society · 2024Article
- Structure and dimerization properties of the plant-specific copper chaperone CCH.Scientific reports · 2024Article
- 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
- An extended interaction site determines binding between AP180 and AP2 in clathrin mediated endocytosis.Nature communications · 2024Article
- Experimental methods to study the structure and dynamics of intrinsically disordered regions in proteins.Current research in structural biology · 2024Review
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- Following the Fate of Lytic Polysaccharide Monooxygenases under Oxidative Conditions by NMR Spectroscopy.Biochemistry · 2023Article
- The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs.RSC advances · 2023Review
- Chemical shift transfer: an effective strategy for protein NMR assignment with ARTINA.Frontiers in molecular biosciences · 2023Article
164 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
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Abstract
RefDB is a secondary database of reference-corrected protein chemical shifts derived from the BioMagResBank (BMRB). The database was assembled by using a recently developed program (SHIFTX) to predict protein (1)H, (13)C and (15)N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins. The predicted shifts were then compared with the corresponding observed shifts and a variety of statistical evaluations performed. In this way, potential mis-assignments, typographical errors and chemical referencing errors could be identified and, in many cases, corrected. This approach allows for an unbiased, instrument-independent solution to the problem of retrospectively re-referencing published protein chemical shifts. Results from this study indicate that nearly 25% of BMRB entries with (13)C protein assignments and 27% of BMRB entries with (15)N protein assignments required significant chemical shift reference readjustments. Additionally, nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. From this study it evident that protein NMR spectroscopists are increasingly adhering to recommended IUPAC (13)C and (15)N chemical shift referencing conventions, however, approximately 20% of newly deposited protein entries in the BMRB are still being incorrectly referenced. This is cause for some concern. However, the utilization of RefDB and its companion programs may help mitigate this ongoing problem. RefDB is updated weekly and the database, along with its associated software, is freely available at http://redpoll.pharmacy.ualberta.ca and the BMRB website.
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