Improving protein order-disorder classification using charge-hydropathy plots

BMC Bioinformatics

Table 5 IDP-Hydropathy scale performance compared to 4 disorder propensity scales, DisProt, TopIDP, FoldUnfold, and B-value.

Method	Sens	Spec	Bal. acc	AUC	F	MCC	PPV	NPV
IDP-Hydro	0.81 ± 0.11	0.98 ± 0.02	0.90 ± 0.07	0.94 ± 0.05	0.84 ± 0.08	0.82 ± 0.09	0.89 ± 0.09	0.96 ± 0.02
DisProt	0.77 ± 0.12	0.97 ± 0.04	0.87 ± 0.08	0.94 ± 0.06	0.80 ± 0.08	0.77 ± 0.10	0.85 ± 0.14	0.96 ± 0.02
TopIDP	0.76 ± 0.11	0.97 ± 0.02	0.87 ± 0.07	0.93 ± 0.04	0.79 ± 0.06	0.76 ± 0.06	0.84 ± 0.07	0.96 ± 0.02
FoldUnfold	0.72 ± 0.12	0.97 ± 0.02	0.85 ± 0.07	0.91 ± 0.07	0.77 ± 0.10	0.73 ± 0.11	0.82 ± 0.11	0.95 ± 0.02
Guy	0.70 ± 0.16	0.97 ± 0.02	0.84 ± 0.09	0.90 ± 0.06	0.75 ± 0.12	0.71 ± 0.13	0.82 ± 0.10	0.94 ± 0.03
B-value	0.67 ± 0.14	0.98 ± 0.02	0.83 ± 0.08	0.91 ± 0.07	0.74 ± 0.11	0.71 ± 0.12	0.85 ± 0.10	0.94 ± 0.02
Kyte-Doolittle	0.61 ± 0.16	0.96 ± 0.03	0.79 ± 0.09	0.87 ± 0.10	0.67 ± 0.13	0.63 ± 0.14	0.78 ± 0.14	0.93 ± 0.03

The accuracy metrics for Guy and Kyte-Doolittle hydropathy scales are also presented as references.
For equations and explanations, see the Methods section at the end of this manuscript:
Sens: Sensitivity
Spec: Specificity
Bal. Acc: Balanced accuracy (average of sensitivity and specificity)
AUC: Area under the curve
F: the F1 score
MCC: Matthew Correlation Coefficient
PPV: Positive Predictive Values
NPV: Negative Predictive Values

ISSN: 1471-2105