## 6 Demonstration
### Visual Analysis of Differences and Stability  
In this section, we comprehensively analyze the analysis of our visualization effects at the level of difference and stability from the following three protein chains. Take T0308 (TBM), T0315 (TBM), and T0353 (FM) as examples to analyze them from the above two levels. The similarity of the RGN prediction results is analyzed from the various factors such as deviation and torsion angle, which can understand its relationship with the loss function and observe where the deviation occurs. Then the rationality of the three chains in the protein conformation was analyzed according to the changing trend of the torsion angle, which judged their stability and observed prediction characteristics of the RGN. According to Section 5, the RGN has reached a high degree of similarity in the TBM prediction method, but it is low in the relatively difficult FM prediction method. For the deviation of the three protein chains, it can be seen that T0315 has the smallest deviation and the alignment area is above 95% (Figure 14), followed by T0308, and T0353 is the longest, so the calculated _TM-Score_ of T0315 is the highest (Figure 15). However, because the coordinates of the residues at both ends of the actual structure of the T0315 chain are abnormal, the distance is too large, and because _dRMSD_ calculates the distance of the entire protein chain, the _dRMSD_ is too large, and _GDT_TS_ is smaller than T0308. For T0353, it can be seen from its _GDT_TS_ that its similarity is very low, but from the change of its torsion angle, there are many regions of relative position consistency, which will lead to the same relative position of the corresponding residues of its predicted structure and actual structure. It will cause its _dRMSD_ to be very small, but we can observe from its deviation change that the alignment area is short, resulting in its _TM-Score_ and _GDT_TS_ being small, and it is judged that T0353 is dissimilar. Figure 13: Comparison of the similarity of two proteins, T0308 and T0315. (**a**,**b**) show the visualization of the tertiary structure after alignment. Red is the predicted structure, gray is the real structure. Charts (**c**,**d**) show the visualization of the distance matrix of the two structures. As for the torsion angle changes of the three protein chains, we can see from Figure 14 that their predicted structures do not conform to physical twists. It shows that even though the _GDT_TS_ of the protein chain is high, that is, the chain is similar, but this is only the global structure (Figure 15). from the smoothness of \(\phi\) angle and \(\psi\) angle and the positive and negative values of the value, the chain still has deficiencies in the local structure, and we can know from the Ramachandran Plot of these three chains (Figure 16), 90% of the predicted structural conformations fall in the disallowed area of The Ramachandran Plot, resulting in unstable conformation. Figure 14: T0308, T0315, T0353 changes in deviation, torsion angle, and _dRMSD_. Blue is the predicted structure, red is the actual structure. Figure 15: Visualization of the three-level structure of T0308, T0315, and T0353. Red is the predicted structure, gray is the real structure. The RGN only adds a loss function to \(dRMSD\); it only penalizes the deviation in the Cartesian coordinate system. So the torsion angle can be changed freely, resulting in a non-physical torsion. Even if the global structure is predicted well, there are still shortcomings in the local structure, which is the cause of the unstable of the tertiary structure of the final protein chain. In addition, the above experimental results are compared with the model quality assessment tool SAVES. The functions of SAVES include verification of protein structure, interatomic interaction, the deviation between atomic volumes, and structural evaluation.