Method
|
Protein dataset
|
Method
|
Peptide dataset
|
---|
RMSD
|
%
|
Outliers
|
RMSD
|
%
|
Outliers
|
---|
IPC_protein
|
0.838
|
0
|
114
|
IPC_peptide
|
0.247
|
0
|
635
|
Toseland
|
0.898
|
15.0
|
131
|
Solomons
|
0.251
|
0.8
|
638
|
Bjellqvist
|
0.922
|
21.5
|
149
|
Lehninger
|
0.256
|
2.4
|
643
|
Dawson
|
0.920
|
20.9
|
156
|
EMBOSS
|
0.322
|
18.8
|
1088
|
Wikipedia
|
0.930
|
23.8
|
157
|
Wikipedia
|
0.413
|
46.3
|
4280
|
Rodwell
|
0.938
|
26.1
|
159
|
Sillero
|
0.426
|
50.9
|
3025
|
ProMoST
|
0.938
|
26.1
|
140
|
Toseland
|
0.427
|
51.2
|
3618
|
Grimsley
|
0.939
|
26.2
|
147
|
Dawson
|
0.432
|
52.9
|
4192
|
Solomons
|
0.947
|
28.5
|
159
|
Thurlkill
|
0.480
|
70.8
|
4017
|
Lehninger
|
0.947
|
28.7
|
160
|
Rodwell
|
0.506
|
81.2
|
4061
|
pIR
|
1.026
|
54.2
|
180
|
DTASelect
|
0.541
|
96.8
|
4902
|
Nozaki
|
1.005
|
47.1
|
169
|
Nozaki
|
0.599
|
124.8
|
4013
|
Thurlkill
|
1.018
|
51.5
|
173
|
Grimsley
|
0.611
|
130.9
|
4609
|
DTASelect
|
1.017
|
51.1
|
167
|
Bjellqvist
|
0.661
|
159.2
|
4672
|
pIPredict
|
1.057
|
65.9
|
173
|
pIPredict
|
1.024
|
497.8
|
8051
|
EMBOSS
|
1.040
|
59.4
|
189
|
ProMOST
|
1.233
|
867.5
|
7999
|
Sillero
|
1.042
|
60.1
|
188
|
pIR
|
1.862
|
4020.9
|
9921
|
Patrickios
|
2.237
|
2405.1
|
645
|
Patrickios
|
1.977
|
5266.8
|
8131
|
Avg_pIa
|
0.940
|
26.6
|
151
|
Avg_pI
|
0.451
|
59.7
|
4600
|
-
aAverage from all pKa sets without the Patrickios (highly simplified pKa set) and IPC sets. Note, that the average pI is calculated on the level of individual protein or peptide
- Protein dataset (IPC_protein trained on 1,743 proteins with 10-fold cross-validation – data in the table above, tested on 581 proteins not used for training – data in Table 1), peptide dataset (IPC trained on 12,662 peptides with 10-fold cross-validation – data in above table, tested on 4,220 peptides not used for training – data in Table 1). Changes in method order in comparison to Table 1 are in bold
- Outliers correspond to the number of predictions for which the difference between the experimental pI and the predicted pI exceeded the threshold of an MSE of 3 for the protein dataset and an MSE of 0.25 for the peptide dataset