@inbook {347, title = {Coarse-Grained Modeling of Protein Dynamics}, booktitle = {Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed.}, volume = {1}, year = {2014}, pages = {55-79}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Simulations of protein dynamics may work on different levels of molecular detail. The levels of simplification (coarse-graining) can range from very low to atomic resolution and 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, membrane proteins, protein-protein interactions and intrinsically unfolded proteins. Presently, these areas represent emerging application fields of CG simulation models.}, keywords = {coarse-grained modeling, protein dynamics}, doi = {10.1007/978-3-642-28554-7_3}, author = {Sebastian Kmiecik and Jacek Wabik and Michal Kolinski and Maksim Kouza and Andrzej Koli{\'n}ski} }