Table 2 Alignment quality results for prob_score and the ProfNet versions trained on different datasets. The ProfNet versions were trained on profile vector pairs from unrelated proteins and protein positions related at family (ProfNet_fam), superfamily (ProfNet_su), fold (ProfNet_fold), and all SCOP levels (ProfNet_all). The training of ProfNet_S was done using superfamily related profile vector pairs as positive examples, and classified by the S-score instead of the binary classifiers used in the other cases. The average MaxSub scores are listed for a test sets with proteins related the family, superfamily or fold levels. The best results are shown in bold.

0.56

0.20

0.063

0.57

0.20

0.064

0.57

0.20

0.070

0.55

0.17

0.057

0.57

0.20

0.067

0.57

0.20

0.072