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ERRAT analysis is used for assessing the protein models which were determined by x-ray crystallography. Next, the value of ERRAT relies upon the statistics of non-bonded atomic interactions in the 3D protein structures. The protein is generally accepted as high quality protein if the percentage is greater than 50%. The ERRAT analysis score result shows that K-ras oncogene protein had the highest at 94.767. Therefore, it can be seen that K-ras oncogene protein has high quality resolution among the protein models. Besides that, the score value for EGFR is 88.010 while 90.374 for TP53 (Figure 1.3).
The Verify3D server was used to reveal the residues in each protein in which EGFR, K-ras oncogene, and TP53 had 98.59%, 100.00%, and 92.96% residues, respectively. Next, the average 3D-1D score of all three proteins are more than 0.2. As a consequence, it specifies that all of the sequences were in line with its protein model (Figure 1.4). Certainly, the resulting energy minimized EGFR, K-ras oncogene protein, and TP53 protein models satisfied the standard for evaluation of protein. Hence, the docking analysis with ligand will be carried out.
Figure 1.1 SOPMA plots for (a) EGFR, (b) K-ras oncogene protein, and (c) TP53.
Table 1.3 Secondary structure of the EGFR, K-ras oncogene protein, and TP53.
| Secondary structure | Alpha helix (Hh) | Extended strand (Ee) | Beta turn (Tt) | Random coil (CC) |
| EGFR | 16.81 | 16.81 | 3.23 | 64.44 |
| KRAS | 43.62 | 21.81 | 7.45 | 27.13 |
| TP53 | 18.79 | 18.21 | 3.18 | 59.83 |
Table 1.4 Composition of α-helix EGFR, K-ras oncogene protein, and TP53.
| Amino acid | Longest alpha helix | Residues | Shortest alpha helix | Number of residues |
| EGFR | α 14 | 14 | α3, α6, α11, α15 | 1 |
| KRAS | α 11 | 20 | α 1, α 10 | 1 |
| TP53 | α 5 | 11 | α 7 | 1 |
Figure 1.2 Ramachandran plots for (a) EGFR, (b) K-ras oncogene protein, and (c) TP53.
Table 1.5 Validation of the EGFR, K-ras oncogene protein, and TP53.
| Structure | Ramachandran plot statistics | Goodness factor | ProQ | ||||||
| Most favored | Additionally allowed | Generously allowed | Disallowed | Dihedral angles | Covalent forces | Overall average | LG score | MaxSub | |
| EGFR | 90.6 | 8.6 | 0.6 | 0.3 | –0.27 | 0.02 | –0.14 | 3.814 | 0.302 |
| KRAS | 90.5 | 8.9 | 0.0 | 0.6 | –0.12 | 0.04 | –0.04 | 4.094 | 0.474 |
| TP53 | 92.9 | 7.1 | 0.0 | 0.0 | –0.16 | 0.07 |
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