Coarse grained modeling of biopolymers and proteins: Methods and applications

Single-molecule mechanics of DNA/RNA, polypeptide and protein has become a new frontier in life sciences. There is an increasing need in participant of researcher in applied mechanics to perform a systematic study on methodologies and basic sciences in molecular mechanics. The wide-applied continuum mechanics may not be applicable in study of the biomolecules. At the same time, the all-atom molecular dynamics method is severely limited by the size and time scales of systems it can simulate. As an alternative, coarse-grained models have recently enjoyed intense interest. Coarse-grained representations combined with enhanced computer power currently allow the simulation of systems of biologically relevant size (submicrometric) and timescale (microsecond or millisecond). In this paper, we reported some progresses we made in the modeling of biomolecules using the coarse-grained methods including, the collapse of biopolymers, the dynamics of HIV-1 protease and the binding dynamics of inhibitors into the protease, aiming to stimulating a broader interest in developing molecular mechanics.