Fig. 5

a The average z-scores obtained for Blosum62, VT160_RA, and VTML200 matrices, and for different weights of combined topology-based matrices obtained using Blosum62 as the basis matrix. The results are shown for helical, beta sheet, and mixed alpha and beta classes. b The average z-scores obtained for Blosum62, VT160_RA, and VTML200 matrices, and different weights of combined topology-based matrices obtained using VT160_RA as the basis matrix. Results are shown for helical, beta sheet, and alpha/beta classes. Z-scores are averaged over all the topologies for each weight for each class. Only improved cases are used to obtain averages. All the z-scores obtained for both improved and other cases are shown in Additional file 1: Tables S4 (a), (b) and (c). The average z-scores for all topologies and the improved topologies are compared in Additional file 1: Table S5. There is no significant difference in z-scores when the weights are changed. It can be seen that the z-scores level off with weight but when the weights are more than ~ 40, z-scores rapidly decrease (not shown)