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Table 1 Comparison of Alignment Accuracies in Contact Overlap, TM-score, and Sequence Similarity

From: High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH

Program

family

superfamily

fold

SABERTOOTH (struct)

53.7/66.9/35.7

30.2/44.5/-13.9

28.4/42.4/-30.6

'best of'

50.1/62.3/40.0

26.8/36.3/-1.2

21.4/29.4/-6.8

HHpred

49.5/62.1/37.5

26.2/36.6/-4.3

20.1/29.2/-10.9

SABERTOOTH (seq)

43.8/55.6/45.7

20.6/29.7/-0.8

18.0/26.9/-12.1

Clustal W

37.0/47.2/55.9

17.0/21.6/22.0

14.8/19.8/18.4

PSI-BLAST

36.5/48.1/51.5

8.50/16.3/15.2

3.7/9.7/13.1

MUSCLE

36.3/47.4/86.1

16.1/21.7/63.5

13.4/19.1/56.7

T-Coffee

35.8/46.6/36.7

16.5/21.2/-7.4

13.8/18.4/-14.8

  1. The table shows the length weighted mean values of contact overlap, TM-score, and sequence similarity (all values multiplied by 100) corresponding to Fig. 1 separated for the three test sets on the major SCOP similarity levels family, superfamily, and fold. The table is sorted by contact overlap on family level. SABERTOOTH structure alignment is added for illustrative purposes, but it is not included in the comparison.