Zhang Haiyan, Neal Stephen, Wishart David S
Faculty of Pharmacy & Pharmaceutical Sciences, University of Alberta, Edmonton, AB, T6G 2N8, Canada.
J Biomol NMR. 2003 Mar;25(3):173-95. doi: 10.1023/a:1022836027055.
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.
RefDB是一个二级数据库，存储了源自生物磁学数据库（BMRB）的经参考校正的蛋白质化学位移数据。该数据库是通过使用最近开发的程序（SHIFTX）来组装的，该程序可根据先前已指定蛋白质的X射线或核磁共振坐标数据预测蛋白质的氢（1H）、碳（13C）和氮（15N）化学位移。然后将预测的位移与相应的观测位移进行比较，并进行各种统计评估。通过这种方式，可以识别潜在的错误指定、排版错误和化学参考错误，并且在许多情况下可以进行校正。这种方法为回顾性重新参考已发表的蛋白质化学位移问题提供了一种无偏差、与仪器无关的解决方案。这项研究的结果表明，近25%已指定碳（13C）蛋白质的BMRB条目和27%已指定氮（15N）蛋白质的BMRB条目需要对化学位移参考进行重大调整。此外，存入生物磁学数据库的蛋白质条目中，近40%似乎至少存在一个指定错误。从这项研究可以明显看出，蛋白质核磁共振光谱学家越来越遵守国际纯粹与应用化学联合会（IUPAC）推荐的碳（13C）和氮（15N）化学位移参考惯例，然而，BMRB中约20%新存入的蛋白质条目仍然被错误参考。这令人有些担忧。不过，RefDB及其配套程序的使用可能有助于缓解这个持续存在的问题。RefDB每周更新一次，该数据库及其相关软件可在http://redpoll.pharmacy.ualberta.ca和BMRB网站免费获取。
