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Jan Jensen edited subsection_Comparison_to_experimental_chemical__1.tex
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For ProCS15 use of ensemble structures lowers the RMSD values for all atom types, with decreases in the range 0.2 - 0.7 ppm for heavy atoms and 0.1 ppm hydrogen atoms. Simmilar improvements are observed for C$\alpha$ and C$\beta$ for CheShift-2, except that the improvement in RMSD (0.5 ppm) is larger compared to ProCS15 (0.3 ppm). This improvement is expected if the NMR-derived ensembles are a more accurate representation of the protein structure in solution than the single x-ray structure.
This is also observed for CamShift, with RMSD-decreases of 0.3 - 1.7 and 0.2 ppm for heavy and hydrogen atoms, respectively. In the case of ppmone, Sparta+, Shaic modest (up to 0.3 ppm) RMSD-decreases are observed for some ensembles but not others and, on balance, the RMSD roughly equally likely to remain unchanged or increase slightly. Finally, for ShiftX2 the RMSD consistently increases (by up to 0.7 ppm) on going from the x-ray structure to the ensembles, with the exception of C$\alpha$ where the RMSD is lowered by 0.1 ppm. We note that the RMSD values predicted with CamShift using the crystal structure are significantly larger than
when using the CHARMM/CMAP structure and that the reduction in RMSD on going to ensembles is at most 0.3 ppm relatively to these values. So, it appears that the use of ensemble structures does not lead to a significant increase in accuracy compared to using a single structure for
\textit{any} of the empirical methods, in contrast to ProCS15 and CheShift-2.
The observations are consistent with earlier observations that the empirical NMR prediction methods tend to be significantly less sensitive to changes in protein structure compared to DFT-based chemical shift predictors or chemical shifts computed using QM methods.
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