Lars Andersen Bratholm edited While_ProCS15_does_not_reproduce__.tex  over 8 years ago

Commit id: 60eccfc976cde50d35d98c4dd6ae195c49ae6712

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Using structures optimized with CHARMM22/CMAP instead of PM6-D3H+ to predict chemical shifts with ProCS15 does also not seem to lead to overall worse agreement with experiment. In fact the results tend to improve slightly (up to 0.5 ppm) for heavy atoms as judged by the RMSD values. Comparison of ProCS15 to CheShift-2, which has also been parameterized against DFT calculations, show fairly similar accuracy for C$\alpha$ and slightly worse accuracy for C$\beta$. The latter observation is perhaps due to the fact that CheShift-2 uses a different (empirical) reference for each residue type. However, this is also the case for C$\alpha$ for which ProCS15 predictions give a lower RMSD value.  Comparison of ProCS15 to the empirical methods (CamShift through ShiftX2) generally show considerably lower RMSD of the empirical predictions  for all atoms types, except H$\alpha$ for GB3 where the accuracy is mostly comparable. The $r$ values are also considerably higher for the empirical methods than for ProCS15 for C$\alpha$ and, especially, C$\beta$, while they are comparable for the remaining atom atoms. As mentioned in the introduction the higher RMSD values generally observed for the DFT-based methods compared to the empirical methods is expected. The important issue in the context of structural refinement against measured chemical shifts is whether the DFT-based methods are more sensitive to relative small differences in structure. While a thorough investigation of this complex issue for ProCS15 will be the subject of future studies, we look at the effect of using different structural ensembles on the accuracy next.