title: Coarse-Grained Protein Models and Their Applications.
abstract: 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 time scales 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.
authors.affiliation: Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kmiecik
authors.affiliation: Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Dominik
authors.initials: D
authors.lastname: Gront
authors.affiliation: Bioinformatics Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences , Pawinskiego 5, 02-106 Warsaw, Poland.
authors.forename: Michal
authors.initials: M
authors.lastname: Kolinski
authors.affiliation: Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.|Department of Medical Biochemistry, Medical University of Lodz , Mazowiecka 6/8, 92-215 Lodz, Poland.
authors.forename: Lukasz
authors.initials: L
authors.lastname: Wieteska
authors.affiliation: Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Aleksandra Elzbieta
authors.initials: AE
authors.lastname: Dawid
authors.affiliation: Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kolinski
mesh_terms: D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding
chemical_list: D008565:Membrane Proteins; D010455:Peptides