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Table 3 Comparison of best structural alignment (alignment with maximum TM-score) from Fr-TM-align

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

Average of pairs with best TM-score from Fr-TM-align (200 proteins for each dataset)a
  cRMSDM cR(core)M TMM PSIM % rPSIM % LM covM %
Dataset 1        
CE 4.5 (1.5) 2.5 (0.4) 0.392 (0.207) 39.1 (26.6) 29.3 (26.6) 120.9 59.2
TM-align 4.6 (1.7) 2.3 (0.4) 0.488 (0.163) 46.5 (24.5) 37.1 (27.2) 162.5 70.4
Fr-TM-align 4.5 (1.6) 2.3 (0.4) 0.522 (0.144) 50.0 (23.4) 40.4 (26.5) 170.6 74.5
Dataset 2        
CE 4.8 (1.5) 2.6 (0.4) 0.354 (0.175) 35.8 (24.2) 25.7 (24.1) 108.5 58.0
TM-align 4.7 (1.5) 2.3 (0.4) 0.451 (0.142) 43.9 (21.6) 34.1 (23.3) 139.3 67.5
Fr-TM-align 4.5 (1.5) 2.3 (0.4) 0.497 (0.127) 49.2 (22.0) 39.1 (24.4) 149.1 73.2
  1. a For each protein, we selected the protein pair with the highest TM-score using the Fr-TM-align program. We used the same set of protein pairs selected from Fr-TM-align for comparison with the other programs. cRMSDM, cR(core)M, LM, covM, TMM, PSIM and rPSIM 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.