Journal of Advanced Biomedical Sciences
JABS
Sat, Feb 22, 2025
[Archive]
Winter 2025
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1- Department of Biochemistry, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran , ms.biochemistry2015@gmail.com
2- Department of Cell and Molecular Biology & Microbiology, University of Isfahan, Isfahan, Iran
3- Department of Pharmacognosy, Isfahan University of Medical Sciences, Isfahan, Iran
2- Department of Cell and Molecular Biology & Microbiology, University of Isfahan, Isfahan, Iran
3- Department of Pharmacognosy, Isfahan University of Medical Sciences, Isfahan, Iran
Abstract: (62 Views)
The field of drug design has undergone remarkable advancements with the advent of in silico methods, which utilize computational approaches that accelerate the discovery and development of novel therapeutics. This review provides an overview of two essential techniques in this domain: molecular docking and molecular dynamics simulation. Molecular docking plays a central role in drug design by predicting the binding interactions between a small molecule (ligand) and its target protein (receptor). By leveraging algorithms and scoring functions, molecular docking enables researchers to evaluate the binding affinity and selectivity of potential drug candidates. Through the exploration of various conformations and orientations, molecular docking facilitates the identification of lead compounds for further optimization. In tandem with molecular docking, molecular dynamics simulation has emerged as a powerful tool for studying the dynamic behavior of biomolecular systems over time. By employing physical principles alongside computational algorithms, molecular dynamics simulations provide insights into the conformational changes, flexibility, and stability of protein-ligand complexes. These simulations not only elucidate binding mechanisms but also reveal critical structural features that influence drug-target interactions. This mini-review highlights the applications of molecular docking and molecular dynamics simulation in drug design, emphasizing their utility in lead identification, optimization, and virtual screening. Collectively, the integration of in silico methods—particularly molecular docking and molecular dynamics simulation—has transformed the field of drug design, enabling researchers to significantly accelerate the identification of novel drug candidates while optimizing their therapeutic properties. As computational technologies continue to evolve, these techniques hold immense promise for facilitating the discovery and development of safer, more effective drugs.
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This work is licensed under a Creative Commons — Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)