CheckShift

The construction of a consistent protein chemical shift database is an important step toward making more extensive use of this data in structural studies. Unfortunately, progress in this direction has been hampered by the quality of the available data, particularly with respect to chemical shift referencing, which is often either inaccurate or inconsistently annotated. Preprocessing of the data is therefore required to detect and correct referencing errors. CheckShift provides automatic reference correction for CA, CB, C' and N chemical shifts. CheckShift is based on a comparison between the cumulative distribution function (cdf) of the target chemical shifts with the cumulative distribution function of a set of reference chemical shifts. The closer the two functions are, the higher is the confidence that the chemical shifts are referenced according to the IUPAC standard .

The image below is a screenshot of the CheckShift user interface, after a CheckShift correction was performed. Note: When loading the page for the first time only the Upload and Help button and the status bar will be visible. To get more information about the components click on the part in the image in which you are interested.

Run SimShiftDB Distributions Status Bar Download Picture Upload File Download corrected ShiftX file Total Server Load

Upload

Here you can upload a file containing chemical shifts.

The SHIFTY file format as proposed by Prof. David Wishart , BMRB Star (.str), and TALOS tabular (.tab) are accepted as input. The extensions ".str" and ".tab" are mandatory for BMRB Star and TALOS tabular input files. All files with other extensions are assumed to be in SHIFTY file format.
Note:
When uploading BMRB Star files only the first chemical shift set in the file is used for database searching. For SHIFTY files, just the HA, H, N, CA, CB and C chemical shifts may be defined. The file must not contain any other shift data.

Here you may download sample files for BMRB Star, TALOS or SHIFTY file format.

Get Corrected ShiftX File

Here you may download a corrected version of the uploaded shift file.

Run SimShiftDB

Start SimShiftDB (structure database homology search based on chemical shifts) with the corrected data.

Download Graph

You may also download the currently selected plot in either jpg or png file format.

Status Bar

The status bar show the current status of the CheckShift calculations performed.

Load

The Total Server Load gives you information about the currently utilized capacity of the web-server. Everything below 100% is a good sign and means you will get average response times for your jobs. Above 100% the response time may increase significantly. However, as the server load is only an average measure, this need not be the case , so you can at least give it a try.

Target and Reference Distribution

In this plot the cumulative distribution function of the reference chemical shifts (referenced according to the IUPAC standard) and the target chemical shifts are shown. The target chemical shifts are displayed two times: One time in red which is the distribution function of the original (uploaded) chemical shifts and a second time in green which is the distribution function of the corrected chemical shifts. The better the green dots and the gray reference line match, the more reliable is CheckShift's prediction. The headers of the different tabs show the atom name plus the proposed chemical shift offset (e.g.: CA +3.2 means that the CA shifts shall be corrected by adding 3.2).

References

Simon W. Ginzinger, Marko Skočibušić , and Volker Heun. CheckShift improved: fast chemical shift reference correction with high accuracy. [view]

Simon W. Ginzinger, Fabian Gerick, Murray Coles, and Volker Heun. automatic correction of inconsistent chemical shift referencing. [view]

Robin K. Harris, Edwin D. Becker, Sonia M. Cabral de Menezes, Robin Goodfellow, and Pierre Granger. NMR nomenclature. Nuclear spin properties and conventions for chemical shifts (IUPAC Recommendations 2001)