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PROCHECK server was used to verify the stereo chemical quality and the geometry of protein models through Ramachandran plots (Figure 1.2). Furthermore, it was revealed that all the protein structures are in most favorable region because they had percentage value more than 80% (Table 1.5). Thus, the standard of these proteins was assessed to be immense and reliable. On top of that, PROCHECK analysis disclose that a number of residues such as TYR265 and GLU51 for EGFR while LYS180 for K-ras oncogene protein were located away from energetically favored regions of Ramachandran plot. Besides that, there are no residues found at forbade region for TP53 protein model.

Thereby, the stereo chemical interpretation of backbone phi/psi dihedral angles deduced that EGFR, K-ras oncogene protein, and TP53 have low percentage of residues among the protein models. Moreover, ProQ was utilized in order to validate “the quality” with the usage of Levitt-Gerstein (LG) score and maximum subarray (MaxSub). All the protein models were within the range for LG and MaxSub score according to the outcome exhibited for creating a good model (Table 1.5).

Table 1.2 The number disulfide bonds were quantitated by Cys_Rec prediction program.

Protein	Cys_Rec	Score
EGFR	Cys_9	–13.0
Cys_13	39.2
Cys_17	100.1
Cys_25	98.3
Cys_26	104.2
Cys_30	104.1
Cys_34	90.5
Cys_42	48.2
Cys_45	56.0
Cys_54	58.2
Cys_58	49.5
Cys_85	55.7
Cys_89	54.9
Cys_101	50.4
Cys_105	44.0
Cys_120	63.0
Cys_123	73.3
Cys_127	75.3
Cys_131	61.6
Cys_156	33.0
Cys_264	45.3
Cys_293	43.8
Cys_300	56.5
Cys_304	46.8
	Cys_309	66.0
Cys_317	65.6
Cys_320	60.2
Cys_329	49.1
Cys_333	42.2
Cys_349	42.2
Cys_352	32.9
Cys_356	62.9
Cys_365	70.2
Cys_373	54.2
Cys_376	54.8
Cys_385	35.8
Cys_389	41.2
Cys_411	78.8
Cys_414	85.1
Cys_418	84.4
Cys_422	26.5
Cys_430	3.7
KRAS	Cys_12	–28.5
Cys_51	–74.2
Cys_80	–72.6
Cys_118	–56.4
Cys_185	–15.2
TP53	Cys_124	–19.4
Cys_135	–1.6
Cys_141	–17.9
Cys_176	–9.1
Cys_182	–45.1
Cys_229	–54.4
Cys_238	1.6
Cys_242	–5.5
Cys_275	–34.4
Cys_277	–51.5
Cys_339	–32.8

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	–0.06	4.417	0.454

Figure 1.3 ERRAT plots for (a) EGFR, (b) K-ras oncogene protein, and (c) TP53.