Skip to main content

Table 4 Gapless threading results

From: Reduced alphabet of prebiotic amino acids optimally encodes the conformational space of diverse extant protein folds

Fold class [SCOP #]

\( {\mathfrak{R}}_{\mathrm{prebiotic}}^{\mathbf{10}} \)

\( {\mathfrak{R}}_{\mathrm{best}}^{\mathbf{10}} \)

Rank of \( {\mathfrak{R}}_{\mathrm{prebiotic}}^{\mathbf{10}} \) (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

  1. This table shows computed values of the knowledge-based potential defined in Eq. (12) and the fitness rank of the prebiotic set. The quantity ΔUnative refers to the free energy of the reduced sequence in its correct tertiary structure. The quantity <ΔUincorrect > 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