Team:GreatBay SCIE/3D Model

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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.