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Table 2 Comparison of best structural alignment (alignment with highest CE z-score) from CE

From: Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

Average of pairs with best z-score from CE (200 proteins for each dataset)a
  cRMSDZ cR(core)Z TMZ PSIZ % rPSIZ % LZ covZ %
Dataset 1        
CE 4.0 (1.4) 2.4 (0.4) 0.403 (0.203) 47.5 (23.5) 36.9 (24.5) 118.5 57.8
TM-align 4.0 (1.2) 2.2 (0.4) 0.446 (0.194) 52.8 (21.2) 43.9 (23.9) 129.7 60.9
Fr-TM-align 3.9 (1.1) 2.2 (0.4) 0.459 (0.188) 54.7 (19.9) 45.7 (22.9) 132.6 62.3
Dataset 2        
CE 4.1 (1.4) 2.5 (0.4) 0.366 (0.170) 44.5 (22.4) 34.6 (23.1) 101.7 55.9
TM-align 4.1 (1.3) 2.3 (0.4) 0.408 (0.164) 48.5 (21.0) 39.5 (22.7) 112.4 58.8
Fr-TM-align 4.0 (1.3) 2.2 (0.4) 0.426 (0.161) 50.9 (20.4) 42.0 (22.5) 117.1 60.6
  1. a For each protein, we selected the protein pair with the highest z-score using the CE program. We used the same set of protein pairs selected from CE for comparison with the other programs. cRMSDZ, cR(core)Z, LZ, covZ, TMZ, PSIZ and rPSIZ denotes coordinate RMSD (in Å), cRMSD (in Å) for all aligned pairs that contribute to PSI, number of aligned residues, coverage of aligned residues, TM-score, percentage structural similarity and relevant percentage structural similarity (see Methods). The number in parenthesis is the standard deviation.