<p>The development of cryo-electron microscopy (cryo-EM) has led to significant advancements in the field of structural biology. Specifically, improvements in both hardware and software for cryo-EM have not only addressed previously perceived limitations but have also enabled the accumulation of a vast amount of structural data. The integration of cryo-EM with computational methods, such as molecular docking and molecular dynamics (MD) simulations, has further advanced the study of the molecular mechanisms underlying biological processes. This review explores the transformative contributions of cryo-EM to structural biology and highlights how molecular docking and MD simulations complement experimental data to investigate protein-protein interactions. We discuss the combined application of cryo-EM, molecular docking, and MD simulations, focusing on their roles in advancing structural analysis. Finally, we consider prospective applications, emphasizing the significant influence these techniques on the structural biology. These integrated methodologies provide valuable insights into biomolecular interactions and support structure- and fragment-based drug discovery, offering more accurate and de-tailed structural characterization.</p>