Coarse Grained Protein Modeling (Chapter 20)

Coarse-grained models are experiencing a renewed interest as they grant access to biologically relevant length and time-scales, they allow to single out molecular driving forces from a plethora of biochemical details. Topological models, discussed in the first part of the chapter, are based on the minimal frustration principle that justifies the stability and fast accessibility of the native state. Despite the several underlying approximations, this rich class of models also including Ising-like and Elastic Network Models, has been successfully applied in several contexts, from biomedical problems to the study of mechanical unfolding and translocation. Conversely, the necessity to elucidate the role of the amino-acid sequence on protein folding, in agreement with Anfinsen's postulates, inspires sequence-based models that are reviewed in the second part of the survey. As discussed, each model presents advantages and limitations and the choice of a model is dependent on the problem that must be addressed.