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Table 2 Comparison of the four methods using the three different evaluation schemes for real-value prediction

From: Towards sequence-based prediction of mutation-induced stability changes in unseen non-homologous proteins

Method

Evaluation

r

RMSE

SEQ-NEIGHB

cross-validation ∗

0.63

1.38

 

unseen-mutation

0.59

1.46

 

unseen-residue

0.37

1.60

 

unseen-protein

0.34

1.62

SEQ-FREQ

cross-validation *

0.56

1.47

 

unseen-mutation

0.53

1.53

 

unseen-residue

0.40

1.60

 

unseen-protein

0.33

1.67

EASE

cross-validation *

0.68

1.30

 

unseen-mutation

0.64

1.38

 

unseen-residue

0.44

1.55

 

unseen-protein

0.40

1.60

EASE-AA

cross-validation *

0.58

1.44

 

unseen-mutation

0.55

1.50

 

unseen-residue

0.53

1.46

 

unseen-protein

0.50

1.50

  1. * cross-validation folds were created by dividing mutations randomly (unseen-mutation cross-validation)