## 3 Results and Discussion
### Molecular Docking  
Numerical results of the docking procedure are tabulated in Table S2 of the Supplementary Materials. HADDOCK scores glean over the favorability of the docking of the ligand and receptor and are scored in arbitrary units. The rule of thumb is that the more negative the score, the better. The Z-score indicates the number of standard deviations from which the chosen cluster is located in terms of score. These values are obtained from the top-ranking cluster, the best-scored out of all available clusters in the docking [44]. The HADDOCK scores are plotted in Figure 5.  
From the docking, the top three peptides with the highest HADDOCK score and the lowest-scoring peptide were chosen for further analysis. The choice for these four systems is arbitrary and is based on a hypothesis that the time element may give rise to significant differences in their behavior, as was performed using molecular dynamics simulations. For DR-4, the top HADDOCK scorers are D, E, and B, and the lowest is Q. For DR-5, Q, H, and O, and the lowest is P. For TNFR-1, A, B, and M, and the worst is C. Finally, for the Fas Receptor, O, N, and I, and the lowest is M. Interestingly, Q is shared between DR-4 and DR-5, with it being the worst scorer in the former while the best in the latter. Other  
Figure 5: Plots for the HADDOCK scores and Z-scores from the molecular docking of the top 10 peptides. peptides shared by multiple receptors are B, a good scorer for DR-4 and TNFR-1, and M, a good scorer in TNFR-1, while being the worst in Fas. Death ligands were also docked and their HADDOCK scores compared to the peptides. Three trends were seen, as follows: one wherein the death ligand scored lower than the peptides, as with TRAIL in DR-4; one where the death ligand scored similarly with the peptides, as with TRAIL in DR-5 and Fas-L in Fas; and one with the death ligand scoring higher, as with TNF-\(\alpha\) in TNFR-1. The three-dimensional configuration of the docked peptides to the receptors varies when compared to the actual death ligand, as shown in Figure 6. For DR-4, the receptor monomers tend to bind to the theraphotoxin in a slanted, almost horizontal manner, as the peptides are being encircled by the monomeric chains rather than being vertically clsaped by them as with TRAIL, except E, which exhibits a similar docking profile. The binding of TRAIL to DR-4 is similar to what is observed in crystallographic studies [27]. Figure 6: Docked death receptor and ligand systems. Green, blue, and pink represent chains A, B, and C of the receptor, while yellow represents the ligand. The letter of each docked system correspond to the identity of the peptide that was docked. For DR-5, there is much less horizontal encircling and much more vertical clasping, although H is slanted. Interestingly, the binding of TRAIL to DR-5 is asymmetric, which is unlike what is found in crystallographic studies [28]. This difference may arise from what the server assesses as more favorable upon docking. For TNFR-1, the binding of A is slanted as compared to the other peptides, which are clasped vertically by the monomers. The blue chain in M is slightly skewed in binding as compared to the green and pink chains. The binding of TNF-\(\alpha\) is also similar to what is found in characterization studies. Lastly, for Fas, the binding is skewed and slanted, with O, N, and I being mostly encircled horizontally, while the chains binding M are more diagonal. The binding of Fas-L is characterized by the interaction with the bottom half of the ligand and the top halves of each monomeric chain. Although there are no existing crystallographic structures of the Fas-Fas-L system, when comparing it to the other systems, it looks asymmetric and unlike the nearly perfect binding configuration of DR-4 and TRAIL. The number of hydrogen bonds between the peptide and receptor varies on which residues interact. The number of hydrogen bonds per docked system varies from 8 to 22. The specific interacting residues are enumerated in Table S3.