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Table 3 Prediction Performance as measured by accuracy, sensitivity (sn), and specificity (sp)

From: Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

Kinase family Kinase group N Sequence-only Spatial- information enriched NetPhos 3.1b Disphos 1.3 KinasePhos 2.0
Ser kinases / 363 0.69 ± 0.01
sn:0.76 ± 0.02
sp:0.62 ± 0.03
0.73 ± 0.01
sn:0.73 ± 0.01
sp:0.73 ± 0.02
0.64 ± 0.01
sn:0.70 ± 0.00
sp:0.58 ± 0.01
0.68 ± 0.01
sn:0.47 ± 0.00
sp:0.88 ± 0.03
0.50 ± 0.00
sn:1.00 ± 0.00
sp:0.50 ± 0.00
PKA AGC I 34 0.83 ± 0.03
sn:0.93 ± 0.05
sp:0.83 ± 0.07
0.88 ± 0.02
sn:0.86 ± 0.05
sp:0.80 ± 0.07
0.82 ± 0.02
sn:0.82 ± 0.00
sp:0.81 ± 0.05
  0.71 ± 0.03
sn:0.65 ± 0.00
sp:0.75 ± 0.04
PKC AGC II 31 0.82 ± 0.02
sn:0.76 ± 0.03
sp:0.87 ± 0.03
0.82 ± 0.02
sn:0.80 ± 0.03
sp:0.81 ± 0.04
0.72 ± 0.02
sn:0.58 ± 0.00
sp:0.86 ± 0.04
  0.64 ± 0.03
sn:0.61 ± 0.00
sp:0.66 ± 0.04
MAPK CMGC II 12 0.89 ± 0.04
sn:1.00 ± 0.00
sp:0.79 ± 0.08
0.89 ± 0.04
sn:0.88 ± 0.15
sp:0.79 ± 0.08
0.69 ± 0.02
sn:0.42 ± 0.00
sp:0.96 ± 0.04
  0.61 ± 0.05
sn:0.50 ± 0.00
sp:0.64 ± 0.08
CKII CMGC IV 19 0.70 ± 0.03
sn:0.79 ± 0.18
sp:0.60 ± 0.18
0.74 ± 0.04
sn:0.88 ± 0.15
sp:0.61 ± 0.14
0.74 ± 0.02
sn:0.53 ± 0.00
sp:0.94 ± 0.04
  0.62 ± 0.03
sn:0.47 ± 0.00
sp:0.67 ± 0.07
Thr kinases / 134 0.68 ± 0.01
sn:0.55 ± 0.04
sp:0.87 ± 0.04
0.69 ± 0.01
sn:0.61 ± 0.04
sp:0.80 ± 0.04
0.63 ± 0.01
sn:0.49 ± 0.00
sp:0.77 ± 0.02
0.66 ± 0.03
sn:0.49 ± 0.00
sp:0.83 ± 0.05
0.50 ± 0.00
sn:1.00 ± 0.00
sp:0.50 ± 0.00
Tyr kinases / 253 0.65 ± 0.01
sn:0.67 ± 0.06
sp:0.63 ± 0.06
0.67 ± 0.01
sn:0.51 ± 0.03
sp:0.81 ± 0.03
0.62 ± 0.01 sn:0.54 ± 0.00
sp:0.71 ± 0.01
0.53 ± 0.02
sn:0.29 ± 0.01
sp:0.77 ± 0.05
0.50 ± 0.00
sn:1.00 ± 0.00
sp:0.50 ± 0.00
SRC PTK I 24 0.70 ± 0.03
sn:0.74 ± 0.15
sp:0.66 ± 0.16
0.75 ± 0.03
sn:0.77 ± 0.09
sp:0.72 ± 0.10
0.57 ± 0.01
sn:0.17 ± 0.00
sp:0.98 ± 0.10
  0.70 ± 0.04
sn:0.83 ± 0.00
sp:0.66 ± 0.04
unspecific predictor   750 0.66 ± 0.01
sn: 0.65 ± 0.01
sp:0.69 ± 0.02
0.69 ± 0.01
sn:0.60 ± 0.03
sp:0.78 ± 0.03
0.63 ± 0.01
sn:0.61 ± 0.01
sp:0.66 ± 0.01
0.62 ± 0.01
sn:0.42 ± 0.01
sp:0.83 ± 0.03
0.50 ± 0.00
sn:1.00 ± 0.00
sp:0.50 ± 0.00
  1. Results from the cross-validation of the various prediction approaches. The sequence-only and Spatial-information enriched methods were developed as part of this study and compared to to NetPhos 3.1b that includes the kinase-specific predictor NetPhos/K, Disphos1.3 and KinasePhos2.0. The size of the negative set was adjusted to the size of the positive sites, ensuring equal sizes of the sets and a comparison to original reports of accuracies of alternative prediction approaches. In the case of the kinase unspecific prediction of KinasePhos2.0, all sites were predicted to be phosphorylated by at least one kinase. Best performing methods are printed in bold-face. Sn denotes sensitivity, while sp denotes the specificity for the stated accuracy.