Table 1 MCC-values and the corresponding Z-scores for prob_score and 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 (family, superfamily and fold) (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 results are shown for protein pairs related on family, superfamily and fold level. The best results are shown in bold.

From: ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins