## 4 Conclusions  
The application of a network of links interconnecting nodes that mimic the protein atoms (all-atom model) or residues (coarse-grained model) was studied in this work. The static geometrical description made available in the PDB file for the crystallized hen-egg white lysozyme was used to analyze the dynamic properties of the resulting structure. Each node was interconnected with close neighbors by establishing a sphere of influence, i.e., a cutoff radius that defines the connectivities. The all-atom geometry was composed of 1000 heavy atoms, while the coarse-grained domain comprised the 129 amino acids of the protein. Various conventional dynamic properties were extracted and analyzed with different tools. Regarding the application of the all-atom model, it was found that the computed B-factors displayed an overall behavior similar to the experimental ones. Some spurious peaks were created, but the protein flexibility was globally well captured with this modeling technique. The effect of the number of eigenvectors considered in the B-factor summation process was also investigated and discussed. It was found that the application of only the initial low-frequency modes is not necessarily sufficient enough to capture all the significant peaks. It was shown that more than half of the 2994 extracted modes should be used to obtain a good approximation with the experimental values when using the all-atom representation. The collectivity index analysis showed that the modes are relatively localized with the all-atom modeling strategy. Additionally, it was observed that the mode shapes do depend on the selected horizon. However, lower cutoffs presented the classic cleft mode observed in many other studies. From the 15 A case onwards, this specific modal shape was lost, and collective motions were also reduced. Therefore, it seems that increasing the number of elastic connections creates a locking process that only allows localized movements to occur in single modes. The range of frequencies from the first mode up to the last one was found to span within one order of magnitude. Moreover, it was observed that all the 2994 natural frequencies were highly packed. The increase of the adopted cutoff value was found to increase the structure's global stiffness, reducing even further the spanning of the full frequency range. These frequency spectra tended to follow a clear normal distribution for the cases between 12 A and 15 A. The literature indicates this behavior due to the similar form and constituents composing globular proteins. However, the reasons for the presence  
Figure 13: The modes and the natural frequencies for the whole spectrum of 381 modes. All cases based on the different cutoffs are displayed. A closer view of the first 50 modes is also presented at the top-left of the main plot. The six histograms show the frequency distribution for each cutoff. of a normal distribution are still in debate without a clear answer to that. This discussion can be deepened in future studies. Regarding the application of the coarse-grained model, it was found that the application of the real residue masses to the structure's nodes, which correspond to the actual masses of each amino acid, did not lead to significant changes in the dynamic output. By comparison with the previous work from [PERSON] et al. (2015), who considered a uniform mass for all the residues, no significant difference was found as far as the mode shapes and B-factors profiles were concerned. This leads to conclude that the structure's mass is reasonably uniformly distributed within a globular protein; therefore, there is no need to consider the actual mass values when adopting a coarse-grained modeling approach. The main divergence from the previous work originated when considering a different location for the node representing each amino acid within the structure. The usual strategy for this purpose has relied on the node's location at the position of the C\({}^{\alpha}\) atom ([PERSON] et al., 2016; [PERSON], 2017; [PERSON], 2017).