Table 3 Improvement of protein secondary structure prediction with the addition of a "residue-specific" RSA threshold for Chou-Fasman and HMM method.
From: Impact of residue accessible surface area on the prediction of protein secondary structures
| Â | Applied Threshold | |||
|---|---|---|---|---|
| Â | Chou-Fasman | HMM | ||
| Â | Mean | Median | Mean | Median |
A | 11.89 | 10.43 | -5.29 | -5.41 |
C | 3.33 | 1.27 | 4.26 | 4.93 |
D | 11.73 | 10.77 | 5.81 | 6.66 |
E | 9.16 | 8.56 | -3.55 | -3.76 |
F | -0.32 | -0.39 | 1.12 | 1.55 |
G | 9.11 | 6.72 | 12.79 | 14.25 |
H | 10.92 | 12.61 | 2.83 | 3.28 |
I | -0.01 | -1.45 | 0.08 | 0.41 |
K | 8.31 | 5.76 | 0.25 | 0.35 |
L | 1.08 | 1.21 | -3.53 | -3.49 |
M | 0.17 | -0.40 | -3.60 | -3.62 |
N | 8.38 | 8.71 | 7.20 | 8.12 |
P | 12.32 | 10.08 | 11.97 | 13.56 |
Q | 10.35 | 9.07 | -2.55 | -2.53 |
R | 9.67 | 8.32 | -1.21 | -1.10 |
S | 11.61 | 7.89 | 5.07 | 5.79 |
T | 1.68 | 0.16 | 5.22 | 6.10 |
V | -0.23 | -0.61 | 2.20 | 2.50 |
W | -0.57 | -0.71 | -0.78 | -0.84 |
Y | 0.74 | 0.68 | 0.87 | 1.04 |
Total Improvement | 9.99 | 8.69 | 3.37 | 3.92 |
| Â | Applied Threshold | |||
| Â | Chou-Fasman | HMM | ||
|  | Tertile | Mean ± standard deviation | Tertile | Mean ± standard deviation |
A | 12.15 | 12.50 | -4.31 | -2.69 |
C | 2.64 | 1.76 | 3.85 | 2.93 |
D | 13.61 | 13.17 | 8.94 | 6.01 |
E | 10.35 | 9.48 | -1.97 | -1.04 |
F | -0.23 | -1.88 | -0.17 | 1.37 |
G | 9.29 | 8.80 | 18.48 | 13.14 |
H | 12.23 | 11.60 | 4.48 | 3.76 |
I | -0.51 | 0.09 | -0.41 | 0.21 |
K | 8.20 | 8.57 | 1.17 | 1.34 |
L | 0.72 | 0.49 | -3.35 | -1.79 |
M | 1.76 | -0.81 | -1.42 | -1.64 |
N | 8.40 | 8.46 | 10.72 | 7.05 |
P | 12.72 | 14.91 | 17.33 | 11.05 |
Q | 10.40 | 10.65 | -0.73 | -0.66 |
R | 9.57 | 9.99 | 0.28 | 0.37 |
S | 10.10 | 13.09 | 7.41 | 5.28 |
T | 0.52 | 0.60 | 6.44 | 5.30 |
V | -0.28 | -0.20 | 0.97 | 2.02 |
W | -0.87 | -0.63 | -0.50 | 0.44 |
Y | 0.75 | 0.92 | 1.15 | 1.25 |
Total Improvement | 10.23 | 10.34 | 4.32 | 3.62 |