Table 4.

Correlation between different substitution tables and the profile-profile scores. Three tables, BLOSUM62, GONNET and JTT, are derived from sequence alignments while SDM is a structure based table. Three tables derived from ProfNet are also included, using the all (trained on data from all SCOP levels), su (trained on superfamily related data) and S-score (trained on superfamily related data and using the S-score as a classifier instead of a binary classifier) versions. STRUCTAL is a substitution table constructed from the residue matches found in the structurally aligned superfamily-related training set. The highest correlations are shown in bold.

subst. table	prob_score	ProfNet_S
BLOSUM62	0.95	0.75
GONNET	0.93	0.75
JTT	0.87	0.70
SDM	0.89	0.73
STRUCTAL	0.85	0.82
ProfNet_su	0.83	0.96
ProfNet_all	0.83	0.95
ProfNet_S	0.80	1