Skip to main content

Table 3 The cross-validation performances of various algorithms using the alternative secondary structure assignment scheme.

From: Novel methods for secondary structure determination using low wavelength (VUV) circular dichroism spectroscopic data

   SP175 SP175(nr)
Method Parameter α-helix βD Core β-sheet PP-II helix other α-helix βD Core β-sheet PP-II helix other
SIMPLS r 0.968 0.895 0.875 0.687 0.842 0.968 0.883 0.861 0.678 0.839
  δ 0.054 0.022 0.034 0.036 0.052 0.055 0.023 0.036 0.036 0.052
PCR r 0.966 0.894 0.876 0.684 0.841 0.965 0.881 0.862 0.677 0.837
  δ 0.056 0.022 0.034 0.036 0.052 0.057 0.023 0.035 0.036 0.053
PLS r 0.971 0.889 0.863 0.641 0.839 0.970 0.881 0.854 0.628 0.833
  δ 0.052 0.023 0.035 0.038 0.052 0.053 0.024 0.036 0.039 0.053
PLS-opt r 0.971 0.868 0.867 0.702 0.835 0.969 0.856 0.846 0.696 0.830
  δ 0.053 0.025 0.035 0.035 0.053 0.054 0.026 0.037 0.035 0.054
SELMAT3 r 0.957 0.911 0.811 0.640 0.827 0.954 0.888 0.751 0.530 0.772
  δ 0.063 0.021 0.041 0.039 0.054 0.065 0.023 0.047 0.043 0.062
SELMAT1_norm r 0.958 0.923 0.815 0.669 0.796 0.955 0.903 0.774 0.668 0.771
  δ 0.062 0.019 0.040 0.037 0.058 0.065 0.021 0.045 0.037 0.062
  1. The (nr) tag indicates that the cross-validation was carried out under the more stringent conditions where no proteins in the training set with the same CATH homologous superfamily as that of the test protein were included. The best results for each secondary structure type for the standard and non-redundant datasets are shown in bold.