Table 1.

Properties of global structural alignments for PDB200, QS, PDB250, Taylor, Trovato, and Zhou sets

Target	Template Library	Fraction of targets with TM-score ≥0.4	Average Coveragea,c	Average TM-score	Average Number of Gaps per Targetb,c	Average Gap Length per Targetc	Average Number of Gaps per Templateb,c	Average Gap Length per Templateb,c
PDB200	PDBe	1.00	0.86	0.65	1.19	4.87	3.98	16.7
PDB200sm	PDBsmf	1.00	0.89	0.70	1.01	4.81	2.86	17.0
PDB200	PDB300	1.00	0.84	0.64	1.27	5.19	3.05	11.2
PDB200sm	PDB300smf	1.00	0.87	0.69	1.08	5.13	2.83	16.3
QS200	PDB	0.99	0.78	0.44	2.97	6.63	10.6	22.6
QS200sm	PDBsm	0.99	0.82	0.51	2.24	7.62	6.40	28.0
QS200	PDB300	0.85	0.76	0.43	2.96	6.84	8.20	14.3
QS200sm	PDB300sm	1.00	0.80	0.49	2.46	8.15	5.43	17.9
PDB250	QS300	0.71	0.78	0.42	2.31	6.36	10.11	13.8
PDB250sm	QS300sm	0.94	0.79	0.48	2.37	8.37	6.99	17.6
PDB250	TASSER model	0.98	1.00	0.71	-	-	-	-
Taylor Set	PDBd	1.00	0.83	0.53	1.78	7.37	8.55	23.8
Taylor Set	PDBsmf	1.00	0.85	0.59	1.53	7.64	5.85	27.6
Taylor Set	PDB300	1.00	0.79	0.52	2.02	8.07	6.61	15.3
Taylor Set	PDB300smf	1.00	0.83	0.57	1.67	8.65	4.94	18.7
Trovato Set	PDBd	1.00	0.87	0.52	0.61	3.42	5.02	26.2
Trovato Set	PDBsmf	1.00	0.90	0.59	0.44	2.84	2.69	29.4
Trovato set	PDB300	1.00	0.85	0.51	0.66	3.78	4.66	18.6
Trovato set	PDB300smf	1.00	0.89	0.58	0.46	3.04	2.64	21.6
Zhou Set	PDB	1.00	0.81	0.54	1.44	7.37	6.18	23.9
Zhou Set	PDBsmf	1.00	0.86	0.59	1.22	6.71	4.55	26.4
Zhou Set	PDB300	0.98	0.78	0.52	1.70	8.38	5.13	16.9
Zhou Set	PDB300smf	1.00	0.83	0.57	1.30	7.46	3.85	19.1

^aFraction of residues in the target sequence that are part of the best structural alignment.

^bOnly gaps >3 residues are considered.

^cOnly templates with a TM-score ≥ 0.4 are considered.

^dStructural alignments to the entire PDB library without chain length restrictions.

^eAll template structures with a sequence identity >15% to the target are excluded.

^fStructural alignments are of the target and template are performed using the smoothed chain contour generated by eq.2a and 2b.