Table 1. Comparison of loop modeling results by the average RMSD of main chain atoms (N, C_α, C, and O) of loops in angstroms (Å) on test sets of varying environmental accuracies measured by E-RMSD.

Framework	Loop set (No. residue)	E-RMSD (Å)	Loop Sampling1)			Extended Sampling1)
			GalaxyLoop		HLP2)	HLP-SS2)	Rosetta-KIC3)	NGK4)
			PS2	PS1
Crystal structure	Set 1 (8)5)	0±0	0.9±0.7	1.3±0.8	1.2±1.5	1.4±1.2	-	0.5±0.3
	Set 1 (12)6)	0±0	1.6±1.3	2.4±1.3	1.2±1.2	1.4±1.4	1.9±1.9	1.7±1.8
	Set 2 (12)7)	0±0	2.5±2.0	3.2±1.9	-	-	2.2±2.1	2.0±2.3
Side chain-perturbed	Set 1 (8)5)	0.9±0.3	1.3±0.9	1.8±1.5	2.4±1.6	1.3±1.5	-	0.5±0.3
crystal structure	Set 1 (12)6)	1.0±0.2	2.1±1.6	3.0±1.4	2.6±1.9	1.7±1.4	1.6±1.4	1.7±1.8
Backbone-perturbed	Set 1 (8)5)	1.9±0.6	2.0±1.8	2.2±1.5	-	-	-	2.1±1.8
crystal structure	Set 1 (12)6)	2.2±0.9	2.1±1.4	3.2±1.4	-	-	-	2.3±2.0

Standard deviations are also reported.

¹⁾Loop sampling methods sample only the loop region, while extended sampling methods sample surrounding side chains in addition to the loop.

²⁾Taken from Sellers et al. [15].

³⁾Taken from Mandell et al. [16].

⁴⁾Results of the best-score models out of 500 models sampled for each target following the protocol provided by Stein et al. [18] with Rosetta v3.5.

The results for the crystal structure set and the side chain-perturbed set are the same for NGK because extended sampling of loop environment was used for both sets.

⁵⁾Loop sets taken from Jacobson et al. [10]. See Tables S1 and S2 for the list of loops.

⁶⁾Loop sets from Zhu et al. [34]. See Tables S1 and S2 for the list of loops.

⁷⁾Loop set from Fiser et al. [1]. See Tables S3 for the list of loops.