Molecular Dynamics: The Computational Molecular Microscope

Document Type : Editorial


1 School of Medicine, Mashhad University of Medical Sciences, Mashhad, IR Iran

2 Beckman Institute for Advanced Science and Technology, Biophysics and Computational Biology Center, University of Illinois at Urbana-Champaign, Urbana, United States



Advanced technologies in molecular biology and modern experimental biophysics heavily rely not only on the knowledge of structure of essential proteins but also on their structural dynamics. The function of these bimolecular systems and the pathways along which the biological phenomena take place can be determined based on the knowledge of the molecular structure and behavior. As such, the simple view of rigid biological structures could not adequately describe the intra-molecular motions and their essential role in conformational changes that are critical to the function. Molecular dynamics simulation offers a computational microscope allowing us to visualize the motion of molecular systems at high spatial and temporal resolutions, thereby providing new opportunities for developing a deeper understanding of the dynamics of biological systems at atomic resolution where no experimental microscope is currently applicable.