Table 1. Evaluation of designed sequences.

Methods	TM-scorea	RMSDb	Normalized relative error (NRE)				Sequence Identity
			SSc	Φ	Ψ	SAd	All	Core
PBMe	0.74	4.14 Å	2.40	0.43	1.01	0.41	21%	35%
EvBMf	0.82	2.82 Å	0.48	0.26	0.30	0.04	27%	35%
EBMg	0.87	2.12 Å	0.33	0.14	0.22	0.02	28%	41%

Data is averaged over 87 test proteins. The details on each protein can be found at Table S2, S3, S4.

^aTM-score between the first I-TASSER model and the target scaffold.

^bRMSD between the first I-TASSER model and the target scaffold.

^cSS: Secondary structure.

^dSA: Solvent accessibility.

^ePBM: Physics-based method using FoldX.

^fEvBM: Evolution-based method using only evolutionary terms in Eq. (1).

^gEBM: Evolutionary based method using both evolutionary and physics-based terms in Eq. (3).