TABLE 1.

Summary of results from PROSPECTOR_3, refinement by nonoptimized TASSER, and comparison with the best structural alignment between the template/model to native

				〈Coverage (in %)〉*			〈RMSD to native (in Å)〉†
Sequence Identity		N	Template selected	Tali	Taln	Maln	Tali	Mali	Ment	Taln	Maln
35–40%	Easy set	269	Top2 + consensus	96			2.5(1.6)	1.9(1.2)	2.2(1.4)
	TMalign A				94	95				1.7(0.4)	1.6(0.4)
	TMalign F				95	98				1.7(0.4)	1.7(0.4)
	Medium	1	Top five	55			1.3	2.7	7.6
	TMalign A				55	51				1.3	2.4
	TMalign F				55	63				1.3	3.2
40–50%	Easy set	219	Top2 + consensus	97			2.4(2.3)	2.0(2.1)	2.4(2.2)
	TMalign A				94	95				1.6(0.5)	1.5(0.5)
	TMalign F				95	98				1.5(0.5)	1.6(0.5)
50–60%	Easy set	150	Top2 + consensus	97			2.0(1.5)	1.9(1.7)	2.3(2.3)
	TMalign A				95	95				1.4(0.6)	1.4(0.5)
	TMalign F				95	97				1.4(0.6)	1.6(0.5)
60–70%	Easy set	111	Top2 + consensus	97			1.9(1.7)	1.8(1.6)	2.2(2.2)
	TMalign A				95	96				1.2(0.5)	1.4(0.5)
	TMalign F				96	98				1.2(0.5)	1.5(0.5)
70–80%‡	Easy set	60	Top2 + consensus	97			2.2(2.6)	2.0(1.9)	2.4(2.2)
	TMalign A				94	95				1.2(0.7)	1.5(0.6)
	TMalign F				95	97				1.2(0.7)	1.5(0.6)
	Medium	2	Top five	83			5.0	1.8	4.8
	TMalign A				73	83				2.2	1.6
	TMalign F				73	90				2.1	2.0
80–90%	Easy set	88	Top2 + consensus	97			1.8(2.0)	1.9(1.5)	2.1(1.6)
	TMalign A				95	95				1.1(0.6)	1.5(0.7)
	TMalign F				96	98				1.1(0.6)	1.6(0.7)
	Medium	1	Top five	86			2.4	7.0	11.5
	TMalign A				79	62				1.9	1.6
	TMalign F				81	64				2.0	1.7

N, number of targets in the category.

^*Alignment coverage on average for the best template that has highest TM-score to native is under the column T_ali. The coverage for the structural alignment of the best template to native and the final model to native is under columns T_aln and M_aln, respectively.

^†RMSD of the best initial template and best model among top five clusters, T_ali, template structure with RMSD calculated over aligned region; M_ali model with RMSD calculated over aligned residues; M_ent, model with the RMSD calculated over the entire chain. T_aln and M_aln refer to the structural alignment of the best template to native and the final model to native, respectively. TMalign (A) and TMalign (F) refer to the best structural alignment using TM-align for the aligned region of the template/model (by PROSPECTOR_3) to the native and full-length template/model to the native, respectively. T_aln and M_aln refer to the structural alignment of the best template to native and the final model to native, respectively. The number in parentheses is the standard deviation for the given average RMSD.

^‡Anomaly in the 70–80% range is because of two targets (1mvkA and 1tud_), which have a very high RMSD of 12.5 Å and 10.9 Å, respectively, from native. If we do not consider them, the average RMSD is reduced to 1.8 Å, and the trend of decreasing RMSD with increasing sequence identity is preserved. These two proteins have very few secondary structures and are small proteins.