## 8 Case Study and Feedback
### Case Study
#### 8.1.2 Progressive Visual Analysis Results of Molecular Pockets
The zoom operation of the magnifying glass component can display the changes of pocket characteristics in any time period and the effect of the magnifying glass component. Figure 17a shows pocket 4 with 1000 timesteps, and Figure 17b shows pocket 1 with 1000 timesteps. Comparing Figure 17a,b, it can be seen that there are certain differences between the two pockets in some local areas. Enlarge some parts with obvious differences, as shown by the vertical dotted line in Figure 17a,b. Enlarge the range of 100 timesteps locally in pocket 4, as shown in Figure 17c,e,g. Enlarge the range of 100 timesteps locally in pocket 1, as shown in Figure 17d,f,h. It can be seen that the fluctuation of local characteristics in Figure 17c,d is not obvious, the characteristics in Figure 17f are locally delayed from those in Figure 17e, and the characteristics in Figure 17h are also locally delayed from those in Figure 17g. Biochemists believe that these graphs are an effective method for them to visually view dynamic features, and can be used to observe multiple characteristics of pockets, such as the stability of pockets and the correlation between pockets. This method is very helpful for experts seeking to screen alternative pockets. Figure 16: Using the merge component, compare pocket 1 with (**a**) pocket 2, (**b**) pocket 4, (**c**) pocket 6, and (**d**) pocket 8. We use other feature views to analyze the characteristics of pockets with a single granularity. The system supports experts use of the magnifying glass component to select pockets, click to pause amplification, and submit the data to the attribute analysis module. Changes in the distribution of hydrophilic, hydrophobic, and polar amino acids in the pocket can be seen in the pie chart. As shown in Figure 18a, there are fewer dark blue outer rings, whereas there are more light blue outer rings and light yellow orange outer rings in the pie chart. As shown in Figure 18c, there are more dark blue outer rings and light blue outer rings. It shows that the hydrophilic amino acids in pocket 4 are more widely distributed; that is, the hydrophilicity of pocket 1 is worse than pocket 4 in molecular dynamics simulation. Looking at the distribution of inner rings in Figure 18a,c thumbnail pie charts, it is seen that there are more dark blue inner rings and bright red inner rings in Figure 18c than in Figure 18a, indicating that the polarity characteristics of pocket 4 are more obvious than those in pocket 1. Click the thumbnail pie chart, enlarge the timestep of interest, and check the proximity of its physical and chemical properties to amino acids (Figure 18b,d). When the mouse clicks the arrow in the upper right corner of other feature views (red box in Figure 18), the display mode of the pie chart and scatter chart can be switched. The display mode of the scatter chart makes it easy to display the distribution of physical and chemical properties of pockets (Figure 18e). Most of the scatterers are above the y axis, indicating that the hydrophilicity of the two pockets is good, and there are more light-colored scatterers in pocket 4 than in pocket 1, indicating that there are more negatively charged amino acids in pocket 4 than in pocket 1 in the molecular dynamics simulation. The three-dimensional map can assist field experts to observe the morphological characteristics of pockets on a single timestep scale, compare the morphological characteristics of pockets and observe the positional relationship between pockets and molecules. As shown in Figure 19a, orthosteric pocket 1 is a slender pocket located on the shallow surface of GPX4 molecule. As shown in Figure 19b, the opening of pocket 4 is wider than that of normal pocket 1, which is also very conducive to the combination of drug molecules. Figure 17: Features of pocket 4 and pocket 1 enlarged. (**a**) 1000 time steps(pocket 4). (**b**) 1000 time steps(pocket 1). (**c**) 0–100 time steps. (**d**) 0–100 time steps. (**e**) 300–400 time steps. (**f**) 300–400 time steps. (**g**) 900–1000 time steps. (**h**) 900–1000 time steps.