Fig. 6

The average z-scores over all topologies in all helical, all beta sheet, and mixed alpha and beta test cases. (Blosum62 added means Blosum62 combined topology-based matrix and VT160_RA added means VT160_RA combined topology-based matrix) Optimized z-scores are the z-scores corresponding to the weight that gives the best average z-score for each class. Maximum z-score is the best (maximum) z-score obtained for each topology. In other words, optimized average z-scores have used a single weight for the whole class but the maximum average z-scores allow different weights for each topology. The z-score for the remote homology detection when using generic matrices such as Blosum62, VTML200, and VT160_RA can be further improved when structure information is incorporated into substitution matrices