Molecular Dynamics: The Computational Molecular Microscope

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

Keywords:

Molecular Dynamics Simulation , Computational Biology , Structural Bioinformatics