Jan Jensen edited subsection_Comparison_to_experimental_chemical__1.tex  over 8 years ago

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Improvements are 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 PPM\_One, Sparta+, and shAIC modest (up to 0.3 ppm) RMSD-decreases are observed for some ensembles but not others and, on average, the RMSD is 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 \cite{16866544} \cite{Sumowski_2014}, \cite{24082119}, \cite{24391900}  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.