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Table 4 Average percentage of the number of topologies showing improvements for the combined topology-based matrices compared with the three generic matrices (Blosum62, VT160_RA, and VTML200)

From: Fold-specific sequence scoring improves protein sequence matching

  % showing improvements
Blosum62 combined VT160_RA combined
All helical 73 73
All beta sheet 53 49
Mixed alpha and betaa 56 56
  1. The percentage improvements are shown for the Blosum62 combined topology-based matrices and the VT160_RA combined topology-based matrices. The results are shown for all helical, all beta sheet and mixed alpha and beta classes. Both types of combined topology-based matrices perform nearly equally well. The topology-based combined matrices show their best performances for all helical class
  2. aMixed alpha and beta corresponds to the combined group of alpha + beta structures and alpha/beta structures (consistent with CATH)