The PDB structures associated with Alzheimer’s disease—NR1 ligand-binding core (PDB ID: 1PBQ), Human Beta Secretase (BACE1, PDB ID: 4D89), Human Monoamine Oxidase A bound to Harmine (MAO-A, PDB ID: 2Z5X), and Human Acetylcholinesterase (AChE, PDB ID: 4EY6)—were prepared using the Protein Preparation Workflow to ensure proper structural configuration and readiness for subsequent analyses, thereby enhancing the reliability of this study’s results [23,25,27,33,37]. The gene discussed is BACE1; the disease is Alzheimer disease.