# Antimicrobial Peptide Screening from Microbial Genomes in Sludge Based on Deep Learning
## 3 Experiments
### Model Verification  
We modeled all the short peptide sequences in Table 3 and performed molecular docking with the antimicrobial peptide receptor protein (PDB ID: 31 fz). In molecular docking, we employed three evaluation metrics: binding energy (Affinity), RMSD distance from the reference structure (Dist from RMSD), and the RMSD of the best mode (Best Mode RMSD). Binding energy is an indicator of the strength of binding between molecules, where a more negative value typically indicates a tighter binding. Dist from RMSD measures the RMSD distance between the molecular structure and the reference structure, where RMSD reflects the structural similarity of two molecules in three-dimensional space. We selected the conformation with the minimum RMSD distance as the best conformation to ensure its close resemblance to the reference structure. Best Mode RMSD measures the RMSD \begin{table}
\begin{tabular}{c c c c c} \hline \hline
**Model** & **Accuracy** & **Precision** & **Recall** & **F1 Score** \\ \hline LSTM & 0.850 & 0.784 & 0.966 & 0.866 \\ ALSTM & 0.952 & 0.992 & 0.912 & 0.950 \\ Combined & 1 & 1 & 1 & 1 \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Model evaluation parameters. Figure 4: Confusion matrices for LSTM, ALSTM, and fusion models. (**a**) ALSTM, (**b**) Combined, (**c**) LSTM. The four parts of the matrix represent True Positives (TP), True Negatives (TN), False Positives (FP), and False Negatives (FN). value between the best mode selected in the docking simulation and the reference structure, serving as a crucial indicator for assessing the accuracy of the docking model. Considering the three metrics in Table 4, we selected three optimal models corresponding to the peptide sequences LLPRLLARRY, GVREIHGLNPGGCLHTVRLVCR, and FRTTLAPHYLTRLLAPCW. After molecular docking visualization, as illustrated in Figure 5, the structure and binding interactions of the receptor-ligand complex are presented. The first set of images indicates that the complex is primarily supported by van der Waals forces at various binding sites, facilitating interactions between the two molecules. Van der Waals interactions between molecules play a crucial role in intermolecular interactions. These interactions include electrostatic and van der Waals potentials. Studies have shown that van der Waals interactions play a significant role in the attractive forces between molecules, especially when intramolecular covalent bonds are stretched [17]. Additionally, in molecular docking, van der Waals forces significantly increase the binding energy between the two molecules compared to other models, as they involve a small number of pi bonds and attractive charges. \begin{table}
\begin{tabular}{c c c c} \hline \hline
**Model** & **Affinity (kcal/mol)** & **Dist From RMSD 1. b.** & **Best Mode RMSD u. b.** \\ \hline
1 & \(-\)7.4 & 14.129 & 20.562 \\
2 & \(-\)6.2 & 2.168 & 3.017 \\
3 & \(-\)7.3 & 1.326 & 2.133 \\
4 & \(-\)5.9 & 3.126 & 10.883 \\
5 & \(-\)7.0 & 2.274 & 4.324 \\
6 & \(-\)6.9 & 3.077 & 6.023 \\
7 & \(-\)6.9 & 7.883 & 17.806 \\
8 & \(-\)6.3 & 3.657 & 11.755 \\
9 & \(-\)7.0 & 2.395 & 5.414 \\
10 & \(-\)7.0 & 12.373 & 20.499 \\ \hline \hline \end{tabular}
\end{table} 
Table 4: Molecular docking data sheet.