Table 3 Average Z-scores for prob_score and ProfNet_S for the scores for different types of conserved residue pairs. ProfNet_S was trained on superfamily related profile vector pairs and using the S-score as a classifier. The pairs are grouped into pairs with identical residues, positive, zero and negative BLOSUM scores. Finally, the Z-scores for a pair containing one conserved and one non-conserved residue and two non-conserved residues are shown. The highest scores are shown in bold.

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