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

BMC Bioinformatics

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

Average of pairs with best z-score from CE (200 proteins for each dataset)^a
	⟨cRMSD_Z⟩	⟨cR(core)_Z⟩	⟨TM_Z⟩	⟨PSI_Z %⟩	⟨rPSI_Z %⟩	⟨L_Z⟩	⟨cov_Z %⟩
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

^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. cRMSD_Z, cR(core)_Z, L_Z, cov_Z, TM_Z, PSI_Z and rPSI_Z 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.

ISSN: 1471-2105