| Content | |
|---|---|
| Description | Chemical Shift database |
| Data types captured | Re-referenced protein and polypeptide chemical shift assignments |
| Contact | |
| Research center | University of Alberta |
| Laboratory | David S. Wishart |
| Primary citation | RefDB: A database of uniformly referenced protein chemical shifts.[1] |
| Access | |
| Website | http://refdb.wishartlab.com/ |
| Download URL | http://refdb.wishartlab.com/ |
| Miscellaneous | |
| Data release frequency | Weekly with periodic corrections and updates |
| Curation policy | Automatically curated |
The Re-referenced Protein Chemical shift Database (RefDB) [1] is an NMR spectroscopy database of carefully corrected or re-referenced chemical shifts, derived from the BioMagResBank (BMRB) (Fig. 1). The database was assembled by using a structure-based chemical shift calculation program (called SHIFTX) to calculate expected protein (1)H, (13)C and (15)N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins reported in the BMRB. The comparison is automatically performed by a program called SHIFTCOR. The RefDB database currently provides reference-corrected chemical shift data on more than 2000 assigned peptides and proteins. Data from the database indicates that nearly 25% of BMRB entries with (13)C protein assignments and 27% of BMRB entries with (15)N protein assignments require significant chemical shift reference readjustments. Additionally, nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. Users may download, search or browse the database through a number of methods available through the RefDB website. RefDB provides a standard chemical shift resource for biomolecular NMR spectroscopists, wishing to derive or compute chemical shift trends in peptides and proteins.