SHIFTX2 is a web server that predicts 1H, 13C, and 15N protein chemical shifts using the 3D structure (PDB coordinates) of the protein of interest for both backbone and sidechain atoms.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.
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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