Molecular Dynamics Simulations of the Ribosome
Structural biology techniques such as crystallography and cryo-EM produce high resolution snap shots of the ribosome at various stages of protein synthesis. Single molecule studies yield time-resolved measurements with low spatial resolution. Currently, there is no experimental technique capable of producing time-resolved trajectories of the ribosome with atomistic resolution. Computer simulations are critical for furthering our understanding of the ribosome because they fill this gap. We review computational studies of the ribosome, including structural modeling, normal mode calculations, coarse grain simulations, and molecular dynamics simulations. Several success stories have occurred, where predictions based on computer simulations were verified experimentally.