Table 2 Performance of SAP settings on 1206 testing proteins. In the table, column ASA denotes whether accessible surface area is used (Yes/No), column 7PCP denotes whether 7 physicochemical properties are used (Yes/No), column OR denotes output representation is in direct angles (D) or trigonometric ratios (R), column NM denotes normalisation method for input feature encoding is [0,1] range based (R) or Z-score based (Z), WS denotes the best size of the sliding window. Note that the emboldened cells denote the best performance for each combination of ASA and 7PCP while the boxed plus emboldened cells in each respective column denote the best performance among all SAP settings.
From: Enhancing protein backbone angle prediction by using simpler models of deep neural networks
Features | Encoding | \(\phi\) MAE | \(\psi\) MAE | \(\theta\) MAE | \(\tau\) MAE | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ASA | 7PCP | OR | NM | WS | Test | Valid | WS | Test | Valid | WS | Test | Valid | WS | Test | Valid |
N | N | D | R | 5 | 17.14 | 17.66 | 5 | 20.19 | 20.48 | 5 | 6.40 | 6.49 | 5 | 22.74 | 23.02 |
Z | 5 | 16.97 | 17.49 | 5 | 19.99 | 20.24 | 5 | 6.38 | 6.47 | 5 | 22.44 | 22.68 | |||
R | R | 5 | 18.05 | 18.58 | 5 | 21.58 | 21.97 | 5 | 6.70 | 6.81 | 5 | 24.44 | 24.71 | ||
Z | 9 | 17.07 | 17.57 | 5 | 20.14 | 20.43 | 9 | 6.38 | 6.48 | 5 | 22.39 | 22.59 | |||
Y | N | D | R | 9 | 16.08 | 16.51 | 9 | 18.85 | 18.91 | 9 | 6.11 | 6.17 | 9 | 21.83 | 21.35 |
Z | 5 | 16.44 | 16.55 | 5 | 19.36 | 19.56 | 5 | 6.23 | 6.18 | 9 | 21.52 | 21.63 | |||
R | R | 13 | 17.04 | 17.54 | 13 | 19.15 | 19.20 | 13 | 6.38 | 6.18 | 13 | 22.39 | 22.06 | ||
Z | 9 | 16.41 | 16.78 | 9 | 19.26 | 19.94 | 9 | 6.17 | 6.33 | 9 | 21.15 | 21.28 | |||
N | Y | D | R | 5 | \(\overline{\underline{|\mathbf{15.65}|}}\) | \(\overline{\underline{|\mathbf{16.04}|}}\) | 5 | \(\overline{\underline{|\mathbf{18.59}|}}\) | \(\overline{\underline{|\mathbf{18.80}|}}\) | 5 | \(\overline{\underline{|\mathbf{6.07}|}}\) | \(\overline{\underline{|\mathbf{6.16}|}}\) | 5 | \(\overline{\underline{|\mathbf{21.03}|}}\) | \(\overline{\underline{|\mathbf{21.18}|}}\) |
Z | 5 | 16.42 | 16.84 | 5 | 19.59 | 19.84 | 5 | 6.32 | 6.41 | 5 | 22.23 | 22.47 | |||
R | R | 9 | 17.49 | 17.95 | 9 | 21.51 | 21.88 | 9 | 6.68 | 6.79 | 9 | 24.34 | 24.57 | ||
Z | 13 | 16.31 | 16.66 | 13 | 19.68 | 19.87 | 13 | 6.30 | 6.37 | 13 | 22.08 | 22.23 | |||
Y | Y | D | R | 9 | 15.79 | 16.13 | 9 | 18.84 | 18.85 | 5 | 6.12 | 6.17 | 5 | 21.49 | 21.89 |
Z | 9 | 15.87 | 16.55 | 5 | 18.91 | 18.85 | 5 | 6.16 | 6.19 | 5 | 21.12 | 21.71 | |||
R | R | 9 | 16.15 | 16.85 | 9 | 19.30 | 19.91 | 9 | 6.23 | 6.20 | 9 | 21.63 | 21.71 | ||
Z | 9 | 16.70 | 16.51 | 9 | 18.86 | 18.91 | 9 | 6.17 | 6.20 | 9 | 21.74 | 21.65 | |||
