Table 1. Protein scaffolds identified for HCV glycoprotein E1 antigenic site 314–324^a.

#	PDB ID	Chain	Selection	Nres	Nali	Cα RMSD (Å)	TM-score	SA ratio	Clash	Fitting	Votes
1	1JKO	C	Meta-server	46	10	0.41	0.32	0.39	0.00	TM-align (F)	2
2	1LQV	C	Meta-server	33	11	0.57	0.33	0.62	1.53	TM-align (F)	4
3	1VQO	U	Meta-server	53	10	1.59	N/Ac	0.57	0.00	MAMMOTH	3
4	1XU2	R	Meta-server	36	11	1.24	0.26	0.82	1.11	TM-align (F)	3
5	2F60	K	Meta-server	60	11	0.28	0.31	0.56	1.05	TM-align (F)	4
6	3CA7b	A	Cysteine knot	50	8	0.25	0.26	0.55	2.69	TM-align (F)	−
7	3E8Y	X	Meta-server	30	10	0.24	0.42	0.63	4.67	TM-align (F)	2
8	3F2U	A	Meta-server	51	11	1.23	0.31	0.70	0.00	TM-align (F)	3
9	3G7L	A	Meta-server	55	10	0.16	0.30	0.67	1.99	TM-align (F)	3
10	3R8S	Z	Meta-server	58	11	0.49	0.30	0.57	0.00	TM-align (F)	4

^aListed items include scaffold index, PDB identifier, selection method, chain name, number of residues in the scaffold, number of scaffold residues aligned to the epitope, C_α RMSD of aligned residues, solvent accessibility ratio of the epitope-matching region in the scaffold context versus the epitope alone, scaffold-antibody clash score after docking the scaffold into the epitope-antibody complex, fitting algorithm used in the scaffold docking, and the number of algorithmic votes each scaffold received.

^bSelected from the “cysteine knot” structural superfamily or a set of scaffolds identified for the HIV-1 epitope at the V3 base recognized by a broadly neutralizing antibody PGT128 (Ref. ⁴¹).

^cTM-score was only calculated for the scaffolds identified and fitted by TM-align and SPalign, which provide TM-score as part of the output.