Stuctural Modeling
In order to aid our other modeling parts and help to predict the effectiveness of our product, we have used some simulators(Matlab, HDock, RNA Composer) to help predict the structure of our aptamers and the binding models of the aptamer and the HER-II molecule. The followings are some of the models we have predicted.
Negative Aptamer
Figure 1.1: This is the predicted figure of the aptamer used to target HER-II negative cells
Positive Aptamer
Figure 1.2: This is the predicted figure of the aptamer used to target HER-II positive cells
Protein
Figure 1.3: This is the predicted figure of the HER-II protein
Figure 1.4: This is the predicted figure of the HER-II protein
Aptamer-Protein Binding Model
Figure 1.5: This is the predicted figure of the HER-II protein binding with the HER-II positive aptamer
Figure 1.6: This is the predicted figure of the HER-II protein binding with the HER-II positive aptamer
By using the 3DPRC algorithm, we can create a rigid model for the project, which helps to create a rigid model of the molecules binding, providing a direct and clear way to imply the effectiveness of our OncoKiller and also giving some guidance on our experiment conducted on the cell.