Improving protein order-disorder classification using charge-hydropathy plots

BMC Bioinformatics

Table 2 The Order versus Disorder Prediction Performances of 19 Hydropathy Scales Measured by Other Metrics.

Scales	F	MCC	PPV	NPV
Guy	0.75 ± 0.12	0.71 ± 0.13	0.82 ± 0.10	0.94 ± 0.03
Miyazawa	0.74 ± 0.11	0.70 ± 0.12	0.80 ± 0.10	0.94 ± 0.03
Manavalan	0.74 ± 0.11	0.70 ± 0.12	0.80 ± 0.10	0.94 ± 0.03
Sweet	0.74 ± 0.08	0.71 ± 0.08	0.83 ± 0.11	0.94 ± 0.03
Fauchere	0.74 ± 0.08	0.70 ± 0.09	0.83 ± 0.12	0.94 ± 0.02
Rose	0.73 ± 0.12	0.70 ± 0.13	0.82 ± 0.09	0.94 ± 0.03
Black	0.71 ± 0.05	0.67 ± 0.06	0.81 ± 0.12	0.93 ± 0.02
Woods	0.68 ± 0.12	0.64 ± 0.13	0.78 ± 0.12	0.93 ± 0.03
Breese	0.68 ± 0.11	0.63 ± 0.13	0.75 ± 0.15	0.93 ± 0.02
Leo	0.68 ± 0.10	0.64 ± 0.12	0.79 ± 0.15	0.93 ± 0.02
Kyte-Doolittle	0.67 ± 0.13	0.63 ± 0.14	0.78 ± 0.14	0.93 ± 0.03
Roseman	0.64 ± 0.15	0.59 ± 0.17	0.75 ± 0.15	0.92 ± 0.03
Chothia	0.63 ± 0.11	0.59 ± 0.13	0.77 ± 0.15	0.92 ± 0.03
Argos	0.63 ± 0.09	0.59 ± 0.10	0.78 ± 0.13	0.92 ± 0.02
Janin	0.59 ± 0.14	0.55 ± 0.12	0.74 ± 0.11	0.91 ± 0.03
Tanford	0.57 ± 0.14	0.53 ± 0.14	0.72 ± 0.15	0.91 ± 0.02
Eisenberg	0.56 ± 0.16	0.53 ± 0.18	0.74 ± 0.20	0.91 ± 0.03
Welling	0.50 ± 0.15	0.48 ± 0.13	0.78 ± 0.19	0.89 ± 0.02
Wolfenden	0.46 ± 0.11	0.43 ± 0.13	0.69 ± 0.15	0.89 ± 0.02

For equations and explanations, see the Methods section at the end of this manuscript:
F: the F1 score
MCC: Matthew Correlation Coefficient
PPV: Positive Predictive Values
NPV: Negative Predictive Values

ISSN: 1471-2105