title: Coarse-grained molecular simulations of large biomolecules.
abstract: Recently, we saw a dramatic increase in the number of researches that rely on coarse-grained (CG) simulations for large biomolecules. Here, first, we briefly describe recently developed and used CG models for proteins and nucleic acids. Balance between structure-based and physico-chemical terms is a key issue. We also discuss the multiscale algorithms used to derive CG parameters. Next, we comment on the dynamics used in CG simulations with an emphasis on the importance of hydrodynamic interactions. We then discuss the pros and cons of CG simulations. Finally, we overview recent exciting applications of CG simulations. Publicly available tools and software for CG simulations are also summarized.
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo, Kyoto 6068502, Japan. takada@biophys.kyoto-u.ac.jp
authors.forename: Shoji
authors.initials: S
authors.lastname: Takada
mesh_terms: D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009696:Nucleic Acids / Q000032:analysis*; D011506:Proteins / Q000032:analysis*; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D009696:Nucleic Acids; D011506:Proteins