Table 4. Results of Structure Prediction with Multiple Templates Performed by RosettaCM Algorithm^a.

structure	templates	alignment method	Cα-RMSD	GDT-HA
1m0l, best RosettaCM	3wqj	MP-T	1.615	71.15
1m0l, lowest RMSD	3wqj, I-TASSER	MUSTER	1.108	77.31
1m0l, highest GDT-HA	3wqj, Medeller	AlignMe	2.865	85.46
1m0l, 3 templates	4qi1, 3wqj, 1uaz	ClustalO	1.149	73.78
1m0l, 3 templates	4pxk, 4fbz, 4jr8	ClustalO	1.508	62.43
1m0l, 6 templates	BR cluster	ClustalO	1.249	70.59
1m0l, 9 templates	seq. id. ≥ 29%	ClustalO	1.375	69.60
1m0l, 3 templates	4qi1, 3wqj, 1uaz	PralineTM	1.950	67.50
1m0l, 3 templates	4pxk, 4fbz, 4jr8	PralineTM	1.780	68.50
1m0l, 6 templates	BR cluster	PralineTM	1.574	65.53
1m0l, 9 templates	seq. id. ≥ 29%	PralineTM	1.348	73.24
3wqj, best RosettaCM	1uaz	MP-T	0.979	73.61
3wqj, lowest RMSD	1uaz, Medeller	MP-T	0.680	86.75
3wqj, highest GDT-HA	1uaz, Medeller	MP-T	0.680	86.75
3wqj, 3 templates	1uaz, 1m0l, 4qi1	ClustalO	1.235	68.80
3wqj, 6 templates	bacteriorhodopsin cluster	ClustalO	1.924	64.32
3wqj, 3 templates	1uaz, 1m0l, 4qi1	PralineTM	1.504	60.79
3wqj, 6 templates	BR cluster	PralineTM	2.530	65.06
3ug9, best RosettaCM	1m0l	MP-T	4.216	35.96
3ug9, lowest RMSD	1m0l, RosettaCM	MP-T	4.280	35.96
3ug9, highest GDT-HA	1m0l, Medeller	AlignMe	4.731	42.23
3ug9, 5 templates	seq. id. ≥ 20%	ClustalO	13.514	31.28
3ug9, 5 templates	seq. id. ≥ 20%	PralineTM	5.357	38.19
1e12, best RosettaCM	3a7k	AlignMe	1.466	65.48
1e12, lowest RMSD	3a7k, Medeller	AlignMe	1.097	83.89
1e12, highest GDT-HA	3a7k, Medeller	MP-T	1.117	84.10
1e12, 6 templates	seq. id. ≥ 30%	ClustalO	2.260	61.40
1e12, 6 templates	seq. id. ≥ 30%	PralineTM	2.664	59.21

^aThe results are compared with the best models for the same proteins produced by the RosettaCM algorithm based on the single template and with models with lowest C_α-RMSD values and GDT-HA values obtained in the current work.