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

BMC Bioinformatics

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

Average of pairs with best TM-score from Fr-TM-align (200 proteins for each dataset)^a
	⟨cRMSD_M⟩	⟨cR(core)_M⟩	⟨TM_M⟩	⟨PSI_M %⟩	⟨rPSI_M %⟩	⟨L_M⟩	⟨cov_M %⟩
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

^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. cRMSD_M, cR(core)_M, L_M, cov_M, TM_M, PSI_M and rPSI_M 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