Manman Li

Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China
Author    Correspondence author
Computational Molecular Biology, 2024, Vol. 14, No. 6   
Received: 09 Nov., 2024    Accepted: 10 Dec., 2024    Published: 22 Dec., 2024

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular dynamics (MD) simulations have become a pivotal tool in biochemical research, providing profound insights into molecular interactions and dynamic behaviors at the atomic level. This study comprehensively reviews the historical development, fundamental theories, and key techniques of MD simulations, including all-atom simulations, coarse-grained simulations, and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations. Enhanced sampling techniques, such as metadynamics, replica exchange molecular dynamics (REMD), and adaptive biasing force (ABF) methods, are discussed, with a focus on their roles in overcoming energy barriers and sampling rare events. Advanced analysis methods, including trajectory visualization, energy decomposition analysis, and principal component analysis (PCA), are also reviewed, with an emphasis on their applications in protein conformational studies. This study aims to highlight the central role of MD simulations in elucidating biomolecular behaviors and to provide guidance for their future research and technological development.

Molecular dynamics simulations; Biochemical research; Enhanced sampling techniques; Protein conformational studies; Drug design