Table 4.

Gapless threading results

Fold class [SCOP #]	${\mathfrak{R}}_{\text{prebiotic}}^{\mathbf{10}}$			${\mathfrak{R}}_{\text{best}}^{\mathbf{10}}$			Rank of ${\mathfrak{R}}_{\text{prebiotic}}^{\mathbf{10}}$ (out of 184,756)
	ΔUnative/kT	<ΔUincorrect> /kT	ΔUnative/kT - <ΔUincorrect> /kT	ΔUnative/kT	<ΔUincorrect> /kT	ΔUnative/kT - <ΔUincorrect> /kT
backbone interaction domain (Ibb)
All data [1–4, 7]	− 0.2161	0.3590	− 0.5751	− 0.2171	0.3609	− 0.5781	7
α only [1]	− 0.4649	0.2909	− 0.7558	− 0.4647	0.4260	− 0.8907	451
β only [2]	− 0.1014	0.3363	− 0.4377	− 0.1134	0.3983	− 0.5116	455
α/β only [3]	− 0.2453	0.3497	−0.5951	− 0.2482	0.3665	− 0.6148	3
α + β only [4]	− 0.2139	0.3419	− 0.5558	− 0.2154	0.3667	− 0.5821	31
small only [7]	0.0175	0.3503	−0.3328	0.0420	0.4493	−0.4073	4
backbone + contact interaction domain (Itotal)
All data [1–4, 7]	−0.3429	0.6667	− 1.0096	− 0.3676	0.7367	−1.1043	1858
α only [1]	− 1.1000	0.5849	− 1.6848	− 1.1703	0.7039	−1.8743	3260
β only [2]	0.1886	0.7320	−0.5434	0.1724	0.8348	−0.6624	1013
α/β only [3]	− 0.2961	0.6558	− 0.9519	−0.3251	0.7188	− 1.0439	526
α + β only [4]	− 0.2240	0.6939	− 0.9180	− 0.2384	0.7876	− 1.0260	328
small only [7]	0.9708	0.7631	0.2077	0.6454	0.7844	− 0.1390	10,112

This table shows computed values of the knowledge-based potential defined in Eq. (12) and the fitness rank of the prebiotic set. The quantity ΔU_native refers to the free energy of the reduced sequence in its correct tertiary structure. The quantity <ΔU_incorrect > refers to the mean free energy of the shuffled reduced sequence mounted on the same tertiary structure. The difference between these two quantities measures the discriminative ability of the reduced sequence for its correct conformation. The substitution rules for both the prebiotic set and the best reduced set are outlined in Table 2. The rank of the prebiotic set is measured in terms of this discriminative ability, comparing this value to those given by the spectrum of 184,756 alternative reduced alphabets