Fig 1.
A schematic flow showing the various steps involved in the bioinformatics analysis of the KRAS gene.
Fig 2.
SNP distribution in the KRAS gene (absolute counts).
Bars represent the number of SNPs in each category.
Table 1.
Common most damaging nsSNPS in KRAS gene.
Fig 3.
Numbers (n) and percentage (%) of damaging nsSNP predicted by PROVEAN, SIFT, PhD SNP and SNP&GO.
Table 2.
Probability values of deleterious nsSNPs identified in KRAS.
Table 3.
I-Mutant Result for the selected nsSNPs.
Table 4.
Minimized energy values of selected nsSNPs in both wild and mutant protein structure.
Table 5.
Conservation profiles of the selected nsSNPs.
Table 6.
TM-score and RMSD values of 4 selected nsSNPs.
Fig 4.
(3D) Modeling of KRAS Wild type and Mutant Protein.
(A-B) L79P, (C-D) A130P, (E-F) G138E, (G-H) F141L.
Fig 5.
Visualization of the Best Docked KRAS Gene Complex Wild and Mutant Protein (A, C, E) Cyan color represents wild (B, D, F) purple color represents mutant.
Table 7.
ADME analysis using the Swiss ADME server.
Fig 6.
Calculated RMSD values for alpha carbon (Ca) atoms (blue curves) of KRAS protein and protein fit with first ligands (red curves).
In the Fig 6, the (Fig 6A).Wild represents the blue, and red curves represent the ligand (6B). Mutants represent the blue, and ligands represent the red curve. Line representation of the evolution of root mean square fluctuation (RMSF) of KRAS Ca during the MD simulation (6C) Wild, (6D) Mutant.
Fig 7.
Protein Secondary Structure element distribution by residue index throughout the protein structure with first ligand.
Red columns indicate alpha helices and blue columns indicate beta-strands. In the Fig 7, the (Fig 7E) Wild, (7F) Mutant. Timeline illustration of the protein-ligand interactions and contacts (H-bonds, ionic, hydrophobic, water bridges) with first ligand, (7G) Wild, (7H) Mutant.
Fig 8.
Calculated RMSD values for alpha carbon (Ca) atoms (blue curves) of KRAS protein and protein fit with second ligands (red curves).
In the Fig 8, the (Fig 8A). Wild represents the (blue curves), and (red curves) represent the ligand. (8B) Mutant represents the blue, and ligand represents the red curve. Line representation of the evolution of RMSF of KRAS Ca during the MD simulation.(8C) Wild, (8D) Mutant.
Fig 9.
Protein Secondary Structure element distribution by residue index throughout the protein structure with second ligand.
Red columns indicate alpha helices and blue columns indicate beta-strands. In the Fig 9, the (Fig 9E) wild and (9F) mutant. Timeline illustration of the protein-ligand interactions and contacts (H-bonds, ionic, hydrophobic, water bridges) with second ligand (9G) Wild, (9H) Mutant.
Table 8.
Prediction of phosphorylation sites in KRAS protein using GPS3.0 and NetPhos3.1.
Table 9.
Prediction of Ubiquitylation sites in KRAS protein using BDM-PUB and UbPred.