The talk will give examples of results obtained with coarse grained models constructed based on the native state geometry of proteins. Such simplified models allow for molecular dynamics studies of systems at much larger time- and length-scales than in the standard all-atom simulations. The first example is the study of mechanical response of 35 virus capsids of various symmetries and sizes: containing between 8 460 and 135 780 amino acids.
Nanoindentation by a broad AFM tip is modeled as compression between two planes. Plots of the compressive force versus plate separation show a variety of behaviors and molecular effects that are beyond the continuum shell model. A second application is an analysis of properties of proteins with cavities. The third – an analysis of the mechanics of protein degradation by proteasomes in the context of measurement of the stalling force. The fourth – a demonstration of multiple folding pathways in folding of proteins with shallow knots.