%0 Journal Article %J Chemical Reviews %D 2016 %T Coarse-Grained Protein Models and Their Applications %A Sebastian Kmiecik %A Dominik Gront %A Michal Kolinski %A Lukasz Wieteska %A Aleksandra Dawid %A Andrzej Koliński %X The traditional computational modeling of protein structure, dynamics and interactions remains difficult for many protein systems. It is mostly due to the size of protein conformational spaces and required simulation timescales that are still too large to be studied in atomistic detail. Lowering the level of protein representation from all-atom to coarse-grained opens up new possibilities for studying protein systems. In this review we provide an overview of coarse-grained models focusing on their design, including choices of representation, models of energy functions, sampling of conformational space, and applications in the modeling of protein structure, dynamics and interactions. A more detailed description is given for applications of coarse-grained models suitable for efficient combinations with all-atom simulations in multiscale modeling strategies. %B Chemical Reviews %V 116 %P 7898–7936 %G eng %U https://pubs.acs.org/doi/10.1021/acs.chemrev.6b00163 %N 14 %R 10.1021/acs.chemrev.6b00163 %0 Journal Article %J Journal of Chemical Information and Modeling %D 2016 %T Coarse-grained simulations of membrane insertion and folding of small helical proteins using CABS model %A Wojciech Pulawski %A Michal Jamroz %A Michal Kolinski %A Andrzej Koliński %A Sebastian Kmiecik %X The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics and interactions). Here we introduce an extension of CABS representation and force field (CABS-membrane) to the modeling of the effect of biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane. In the resulting trajectories, we have found models close to the experimental membrane structures. We also attempted to select the correctly folded models using simple filtering followed by structural clustering combined with reconstruction to all-atom representation and all-atom scoring. In conclusion, the CABS-membrane model is a promising approach for further development towards modeling of large protein-membrane systems. %B Journal of Chemical Information and Modeling %V 56 %P 2207–2215 %G eng %U https://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00350 %N 11 %R 10.1021/acs.jcim.6b00350 %0 Book Section %B Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed. %D 2014 %T Coarse-Grained Modeling of Protein Dynamics %A Sebastian Kmiecik %A Jacek Wabik %A Michal Kolinski %A Maksim Kouza %A Andrzej Koliński %K coarse-grained modeling %K protein dynamics %X 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. %B Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed. %I Springer Berlin Heidelberg %V 1 %P 55-79 %G eng %R 10.1007/978-3-642-28554-7_3