Review: Coarse-grained model for normal mode analysis of proteins

The preprint provides the summary and/or review of current state-of-art in coarse-grained modeling of protein structures for normal mode analysis. This review summarizes the quasiharmonic analysis, Go model, elastic network model, and recently suggested coarse-grained models for protein structures.

Abstract 

Understanding the protein mechanics is a priori requisite for gaining insight into protein's biological function, since most protein performs its function through the structural deformation renowned as conformational change. Such conformational change has been computationally delineated by atomistic simulations, albeit the mechanics of large protein structure is computationally inaccessible with atomistic simulation such as molecular dynamics simulation. In a recent decade, normal mode analysis with coarse-grained modeling of protein structures has been a computational alternative to atomistic simulations for understanding large protein mechanics. In this review, we delineate the current state-of-art in coarse-grained modeling of proteins for normal mode analysis. Specifically, the pioneered coarse-grained models such as Go model and elastic network model as well as recently developed coarse-grained elastic network models are summarized and discussed for understanding large protein mechanics.