A comprehensive review on molecular docking: methods, applications, and limitations in modern drug discovery

Abstract

Molecular docking is a widely used computational technique for predicting the interaction between small molecule ligands and biological macromolecules. In this study, molecular docking was performed to evaluate the binding affinity, interaction patterns, and potential inhibitory activity of selected compounds against a target protein of therapeutic interest. The 3D structure of the protein was retrieved from the Protein Data Bank, and ligands were prepared using standard energy-minimization protocols. Docking simulations were carried out using validated algorithms to identify the most stable ligand–receptor conformations. Binding energies, hydrogen-bond interactions, hydrophobic contacts, and key amino acid residues involved in ligand stabilization were analyzed. The results indicate that several compounds exhibit strong binding affinity toward the active site, suggesting their potential as lead molecules for further optimization. This study highlights the importance of molecular docking as an efficient tool in early-stage drug discovery and provides a foundation for future in-vitro and in-vivo investigations.

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