Table 3 SRIs predicted from experiment and calculated from structures for proteins and models
From: An improved protein structure evaluation using a semi-empirically derived structure property
Protein name | Method to obtain SRI | Models | SRI | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
Albumin | Predicted through experiment | 1ao6 | 15.10 | 16.08 | 22.41 | 19.45 | 18.14 | 9.48 | 15.04 | 7.80 |
calculated | 1ao6 | 8.22 | 12.68 | 12.31 | 7.70 | 9.91 | 9.27 | 10.09 | 11.62 | |
1 | 9.43 | 11.42 | 7.45 | 12.94 | 13.06 | 9.81 | 7.84 | 9.92 | ||
2 | 14.43 | 11.44 | 7.11 | 12.88 | 11.72 | 11.68 | 9.20 | 9.21 | ||
3 | 8.80 | 11.27 | 7.18 | 13.46 | 13.82 | 10.34 | 9.35 | 8.29 | ||
4 | 11.03 | 15.31 | 13.86 | 8.48 | 14.31 | 8.76 | 7.41 | 11.17 | ||
5 | 9.40 | 11.46 | 8.55 | 13.69 | 13.45 | 9.64 | 8.41 | 9.70 | ||
Cytochrome c | Predicted through experiment | 1new | 5.38 | 5.83 | 4.70 | 2.55 | 5.11 | 4.19 | 3.40 | 3.70 |
calculated | 1new | 3.45 | 5.45 | 4.24 | 2.02 | 3.35 | 2.88 | 3.47 | 3.74 | |
1 | 4.93 | 3.77 | 4.33 | 1.07 | 3.11 | 3.27 | 3.60 | 4.07 | ||
2 | 4.01 | 0.00 | 1.83 | 5.01 | 3.29 | 3.40 | 3.99 | 3.42 | ||
3 | 4.41 | 7.79 | 1.75 | 3.77 | 2.90 | 3.32 | 2.13 | 3.95 | ||
4 | 3.63 | 3.58 | 4.10 | 1.13 | 3.66 | 3.37 | 4.71 | 3.97 | ||
5 | 4.88 | 4.28 | 3.37 | 3.75 | 2.56 | 3.07 | 3.60 | 4.38 | ||
Ferritin | Predicted through experiment | 1ro3 | 4.12 | 5.23 | 4.99 | 3.08 | 6.33 | 3.14 | 3.66 | 3.23 |
calculated | 1ro3 | 0.02 | 3.20 | 1.47 | 0.11 | 2.14 | 1.54 | 2.56 | 1.77 | |
1 | 1.73 | 3.01 | 1.38 | 5.41 | 3.58 | 0.61 | 4.92 | 1.74 | ||
2 | 6.31 | 3.74 | 5.98 | 0.90 | 1.54 | 4.50 | 0.00 | 4.84 | ||
3 | 2.78 | 2.66 | 3.12 | 4.61 | 2.77 | 2.82 | 3.35 | 1.37 | ||
4 | 6.43 | 0.00 | 7.66 | 3.60 | 0.91 | 3.39 | 1.42 | 2.90 | ||
5 | 4.15 | 2.26 | 1.90 | 5.25 | 3.62 | 1.79 | 3.25 | 0.14 | ||
Lysozyme | Predicted through experiment | 2vb1 | 3.51 | 4.29 | 5.36 | 4.05 | 2.84 | 4.06 | 4.84 | 3.93 |
calculated | 2vb1 | 4.19 | 3.32 | 5.05 | 5.32 | 4.23 | 3.05 | 2.92 | 3.83 | |
1 | 4.81 | 4.51 | 2.77 | 3.07 | 4.24 | 3.12 | 3.74 | 3.83 | ||
2 | 4.06 | 4.45 | 2.97 | 3.30 | 4.28 | 2.93 | 3.63 | 3.67 | ||
3 | 3.86 | 4.47 | 2.79 | 3.26 | 4.51 | 3.06 | 3.89 | 3.84 | ||
4 | 4.23 | 4.49 | 3.84 | 3.16 | 4.33 | 3.01 | 3.65 | 3.97 | ||
5 | 5.81 | 4.32 | 2.93 | 3.03 | 4.55 | 2.42 | 3.76 | 4.00 | ||
Insulin | Predicted through experiment | 2h8b | 4.59 | 5.37 | 5.30 | 6.23 | 3.67 | 4.19 | 3.51 | 5.39 |
calculated | 2h8b | 1.66 | 6.09 | 4.07 | 3.96 | 2.54 | 3.20 | 1.92 | 4.20 | |
1 | 2.07 | 7.54 | 5.77 | 2.12 | 9.05 | 2.96 | 3.96 | 5.67 | ||
2 | 5.53 | 4.82 | 3.14 | 1.55 | 8.68 | 5.22 | 2.71 | 1.91 | ||
3 | 5.75 | 2.87 | 2.42 | 5.13 | 6.77 | 3.96 | 2.11 | 4.96 | ||
4 | 7.57 | 3.27 | 6.87 | 2.72 | 5.49 | 4.43 | 1.76 | 5.99 | ||
5 | 6.66 | 3.71 | 4.77 | 2.86 | 1.76 | 3.98 | 3.04 | 5.26 | ||
Hemoglobin | Predicted through experiment | 1a3n | 5.95 | 8.82 | 8.59 | 10.99 | 9.28 | 4.96 | 8.71 | 8.36 |
calculated | 1a3n | 7.80 | 8.31 | 8.69 | 10.99 | 8.73 | 6.31 | 9.10 | 6.73 | |
1 | 8.85 | 9.44 | 9.54 | 10.29 | 7.77 | 9.74 | 7.95 | 11.05 | ||
2 | 9.12 | 6.62 | 9.65 | 8.43 | 4.89 | 7.73 | 8.46 | 9.05 | ||
3 | 9.00 | 5.55 | 9.52 | 7.94 | 4.98 | 7.69 | 8.47 | 8.94 | ||
4 | 7.09 | 8.35 | 8.26 | 8.80 | 8.40 | 6.47 | 9.16 | 6.49 | ||
5 | 9.12 | 6.62 | 9.65 | 8.43 | 4.89 | 7.73 | 8.46 | 9.05 | ||