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SHIFTX2

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SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input. SHIFTX2 combines ensemble machine learning methods with sequence alignment-based methods to calculate protein chemical shifts for backbone and side chain atoms. SHIFTX2 has been trained on a carefully selected set of 197 proteins and tested on a separate set of 61 proteins. Both the training and testing sets consisted of high resolution X-ray structures (<2.1 Angs) with carefully verified chemical shifts assignments. SHIFTX2 is able to attain correlation coefficients between experimentally observed and predicted backbone chemical shifts of 0.9800 (15N), 0.9959 (13CA), 0.9992 (13CB), 0.9676 (13CO), 0.9714 (1HN), 0.9744 (1HA) and RMS errors of 1.1169, 0.4412, 0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. Comparisons to other chemical shift predictors using the same testing data set indicates that SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3X smaller) than any other program.

Please cite the following:
Beomsoo Han, Yifeng Liu, Simon Ginzinger, and David Wishart. (2011) SHIFTX2: significantly improved protein chemical shift prediction. Journal of Biomolecular NMR, volume 50, number 1, 43-57. doi: 10.1007/s10858-011-9478-4.

To operate this server:

1) Indicate whether the query protein is deuterated.
2) Fill in information about pH and Temperature (K).
3) Select the type (all, backbone or proton only) of chemical shift you want to predicted.
4) Select the output format you desire (tabular, comma separated or NMR-STAR format)
5) Indicate whether to combine results from homology-based method (SHIFTY).
6) Type in a valid PDB ID or select a local PDB file.

If a input PDB has multiple chains, the first chain will be predicted as default. You can also specify the chain at the end or PDB ID 2TRXA and 2TRXB.

7) Press the submit button.

Protein is deuterated: Yes No
pH:
Temperature (K):
Select type of chemical shift to be predicted:
Select chemical shift output format:
Combined results with SHIFTY: Yes No
   
PDB ID    OR
Select local PDB file
   
   

 

Problems? Questions? Suggestions? Please contact: shiftx2@wishartlab.com

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