# Antimicrobial Peptide Screening from Microbial Genomes in Sludge Based on Deep Learning
## 3 Experiments
### Model Verification
\begin{table}
\begin{tabular}{c c} \hline \hline
**Prediction Sequence** & **Systematics** \\ \hline LLPRLLARRY & _Clostridiales_ \\ FRVPLAPYVLPPLLARC & _Fervidobacterium_ \\ GVREIHGLNPGGCLHTVRLVCRR & _Caloramator sp._ E03 \\ IRTTLPPYYVFRLLARCW & _Actinobacteria_ \\ FRITPSPHVLPLRGSVC & _Peptostreptococcaceae_ \\ FRITITTHYPHVPLLRLARS & _Romboutsia_ \\ FRTLTFRIVLPRPLGGRC & _Belaproteobacteria_ \\ GLLHTRGIAGGSGLRPLSKIPHCCRP & _Gammaproteobacteria_ \\ RLRRWPCKSCVKTPGSTREVPGKPAGEWCAA & _Thermosiplo africanus_ TCF52B \\ FRITLATYLRLLLPPCS & _Turicbacter sp._ H121 \\ FRSTLAPYGLPRLLGGRC & _Tepidanaerobacter acetaxtoxydans_ Re1 \\ FRTTLAPHYLTRLLAPCW & _Synergistaceae_ \\ RLHPLCYRGCWHRVSRCLFCE & _Actinobacter_ \\ GLHHRSRGMAGGSGLPPLSNIIPHSCHSP & _Bradyrhizobiaceae_ \\ FRITLAPYYPVFRLLHRS & _Rubrobacter xylamophilus_ \\ FRTTLAPYYVPLLLARCW & _Nocardioides sp._ CF8 \\ GLLHSRGIAGGSGLPPLSNIIPHSLP & _Defluviococcus vanus_ \\ \hline \hline \end{tabular}
\end{table} 
Table 3: Short peptide prediction results. In the second and third sets of models, different sites form salt bridges, attractive charges, hydrogen bonds, hydrophobic interactions, pi bonds, and alkyl interactions between molecules. Studies have found that interactions between positively charged amino acid residues and negatively charged residues form salt bridges, enhancing the conformational stability of proteins [18]. Additionally, geometrically optimized salt bridges can accelerate folding speed and decelerate unfolding speed, while poorly shaped salt bridges slow down folding speed and slightly accelerate unfolding speed [19]. Hydrogen bonds play a crucial role in receptor-ligand binding, regulating the degree of protein structural fluctuations, thereby reducing the hydrogen/deuterium exchange (HDX) rate during ligand binding [20]. HDX is an analytical technique that measures the rate at which hydrogen atoms in the protein structure are replaced by deuterium. This replacement process is influenced by protein folding and ligand binding. The decrease in the HDX rate implies a reduction in the protein's dynamics during ligand binding, leading to a more stable structure. This helps minimize errors and instability factors that may arise during the docking process, thereby enhancing the reliability and accuracy of the docking model. Additionally, changes in hydrogen bond energy during the binding process help filter out unrealistic poses during docking and integrate them into the free energy calculation model, improving the accuracy of binding energy calculations [21,22]. Therefore, the docking scores of the two sets of models are relatively high. At the cellular level, antimicrobial peptides exhibit effective antibacterial activity against _Escherichia coli_, primarily achieved by increasing the permeability of the bacterial cell membrane. This process induces morphological changes, swelling, cytoplasmic lysis, and membrane damage in the cells. Such damage results in a decrease in the intracellular ATP concentration and the leakage of essential components, including critical enzymes and nucleic acids. These effects collectively act to disrupt vital physiological functions in bacteria, ultimately leading to bacterial death and, consequently, the manifestation of antimicrobial effects [23]. Figure 5: Visualization of molecular docking for LLPRLLARRY, GVREIHGLNPGGCLHTVR-LVCRR, and FRTTLAPHVLTRLLAPCW. (**a**) Receptor–ligand complex, (**b**) Receptor–ligand complex (zoomed-in view), (**c**) Ligands (antimicrobial peptide candidate), (**d**) Key interactions in the receptor–ligand binding. RMSF (root-mean-square fluctuation) and RMSD (root-mean-square deviation) plots are widely utilized in molecular simulation studies to reveal the dynamics and stability of molecular structures. The RMSF plot illustrates the root-mean-square fluctuations at each atomic position during molecular simulation, while the RMSD plot is used to compare the root-mean-square deviations of atoms between the simulated structure and the reference structure.