Source:
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics, Springer International Publishing:61–87, 2019Abstract
Simulations of protein dynamics may work on different levels of molecular detail. The levels of simplification (coarse-graining) may concern different simulation aspects, including protein representation, interaction schemes or models of molecular motion. So-called coarse-grained (CG) models offer many advantages, unreachable by classical simulation tools, as demonstrated in numerous studies of protein dynamics. Followed by a brief introduction, we present example applications of CG models for efficient predictions of biophysical mechanisms. We discuss the following topics: mechanisms of chaperonin action, mechanical properties of proteins and their complexes, membrane proteinsMembrane proteins and lipids, protein-protein interactions and intrinsically unfolded proteins. These areas illustrate the opportunities for practical applications of CG simulations.