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Table 3 Z-scores for mixed alpha and beta class topologies in test set A: scores obtained for each topology for Blosum62, VT160_RA, and VTML200 matrices are shown in columns 2, 3, and 4

From: Fold-specific sequence scoring improves protein sequence matching

  Z-score
Topology Blosum62 VT160_RA VTML200 Blosum62 combined VT160_RA combined
     Max z-score Max % improvement Max z-score Max % improvement
3.10.20 2.13 2.36 2.17 2.40 2.03 2.39 1.51
3.10.100 3.01 3.67 3.21 5.52 50.48 5.57 51.77
3.10.120 2.78 2.85 2.65 4.14 45.17 4.13 44.83
3.10.129 1.06 1.06 1.11 1.26 13.65 1.14 3.03
3.10.130 2.26 2.62 2.31 4.58 74.78 4.55 73.84
3.10.180 1.62 1.70 1.64 2.58 51.77 2.58 51.89
3.30.30 2.70 3.07 2.75 3.70 20.80 3.75 22.31
3.30.70 2.38 2.73 2.41 3.71 35.56 3.70 35.54
3.30.420 0.14 0.27 0.29 0.29 1.15 0.30 3.54
3.30.428 2.35 2.84 2.47 3.18 11.93 3.26 14.70
3.30.465 2.03 2.11 2.02 2.77 31.30 2.77 31.20
3.30.505 2.52 2.91 2.71 3.13 7.45 3.21 10.27
3.30.1050 2.87 3.16 2.74 3.47 9.85 3.34 5.55
3.30.1520 2.37 2.78 2.48 2.86 2.77 2.82 1.47
3.40.20 3.42 3.81 3.46 4.55 19.33 4.55 19.21
3.40.33 3.05 3.36 2.94 4.90 45.88 4.92 46.64
3.40.109 0.72 0.91 0.29 1.49 64.71 1.46 60.88
3.40.140 4.38 4.79 4.48 5.13 7.03 5.19 8.38
3.40.718 0.42 1.00 0.81 2.75 175.14 2.76 176.14
3.40.980 2.79 3.27 2.85 3.75 14.65 3.81 16.45
3.40.1050 0.07 0.32 0.02 2.23 595.27 2.14 567.18
3.60.21 0.92 0.84 0.79 1.69 83.39 1.67 80.72
3.70.10 3.29 3.77 3.29 4.34 15.15 4.31 14.41
3.90.79 1.86 2.05 1.84 3.01 46.42 2.89 40.90
3.90.730 5.25 5.62 5.34 5.69 1.34 5.67 1.01
  1. Columns 5 and 6 show the maximum z-scores obtained and the maximum percentage improvements obtained when using Blosum62 combined with topology-based matrices. Columns 7 and 8 show the maximum z-scores obtained and the maximum percentage improvements obtained when using VT160_RA combined with topology-based matrices. Maximum percentage improvements are the improvements of combined topology-based matrices over the maximum z-score giving generic matrix for each topology. Only the topologies where z-score improvements were observed for both Blosum62 combined and VT160_RA combined matrices over all three of the generic matrices are shown.