## 5 Multi-Level Visual Design and Analysis of RGN Predicted Results
### Structural Stability  
The stability of a protein is closely related to its specific amino acid sequence, shear processing, and spatial structure. It refers to the ability of the protein to maintain biological vitality and resist the influence of various factors. The previous two levels mentioned that some protein chains in the prediction results of RGN have high similarity, but the stability is unknown. This section aims to analyze the stability of the prediction structure of the RGN.  
The residues are connected by peptide bonds. Because it is a rigid plane, its \(\omega\) angle is basically close to 180\({}^{\circ}\), rarely close to 0\({}^{\circ}\). In the second level, it was mentioned that the change in the torsion angle is the source of all protein conformations, so the torsion angle is an important parameter of the tertiary structure of the protein. The Ramachandran Plot describes whether the torsion angles \(\phi\) and \(\psi\) of the amino acid residues in the protein structure are in a reasonable region and the protein conformation is reasonable. The \(\phi\) and \(\psi\) angles are generally [\(-\)180\({}^{\circ}\), 180\({}^{\circ}\)]. Theoretically, both the C\(\alpha\)-N bond and the C\(\alpha\)-C bond can rotate freely; the rotation of the bond will drive other atoms to rotate together. In fact, due to the space barriers and forces of each group of the molecule, The Ramachandran Plot has areas that are allowed and not allowed (Figure 9).  
It can be seen that the torsion angle of the predicted structure changes more slowly than the actual structure (Figure 6), and the \(\phi\) angle is mostly positive and the \(\psi\) angle is basically negative. This situation causes the torsion angle of the predicted structure to basically fall the disallowed area of the Ramachandran Plot (Figure 10), its conformation is judged to be unreasonable, and the structure is unstable. For the \(\omega\) angle, it does not conform to the characteristic that the rigid plane of the peptide bond is difficult to rotate; that is, there is a non-physical twist. Figure 10 shows the result of the certain chain predicted by the RGN. The left side is the Ramachandran Plot. This picture shows that the actual structure is basically in the core area or the allowable area, but more than 90% of the residues in the predicted structure are in the disallowed area. On the right is the PictorialBar graph. This picture shows the absence of residues in the protein chain, and each element maps to the region of the Ramachandran Plot. It is judged that the predicted structure protein conformation of the chain is unreasonable and unstable structure.  
Figure 8: The line chart shows the change in _dRMSD_ during the assessment stage of the RGN.  
Figure 10: The left side shows the Ramachandran Plot of the certain protein chain, the right side shows the PictorialBar (the upper PictorialBar indicates the predicted structure, the lower PictorialBar is the actual structure) is the area corresponding to the chain residues, and check whether there are missing coordinates. The color of each pictogram corresponds to the area in the Ramachandran Plot, and the left Ramachandran Plot disallowed area (white) is displayed in blue in the pictogram.  
Figure 9: The Ramachandran Plot Region. The red area represents the core area. The yellow region is the allowable region in which the conformation can exist and be stable in stereochemistry. The brown region is the maximum allowable region, in which the conformation can exist stereochemically, but it is unstable. The white area represents the disallowed area; the conformation is not allowed to exist.