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      Coarse-grained molecular dynamics simulations of biomolecules

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          Abstract

          Coarse-grained molecular dynamics (CGMD) simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances such as carbon nanotubes have been suggested. Here we briefly discuss a method for CGMD system configuration and the types of analysis and perturbations that can be performed with CGMD simulations. We also describe specific examples to show how CGMD simulations have been applied to various situations, and then describe experimental results that were used to validate the simulation results. CGMD simulations are applicable to resolving problems for various biological systems.

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          Coarse-grained models for proteins.

          Coarse-grained models for proteins and biomolecular aggregates have recently enjoyed renewed interest. Coarse-grained representations combined with enhanced computer power currently allow the simulation of systems of biologically relevant size (submicrometric) and timescale (microsecond or millisecond). Although these techniques still cannot be considered as predictive as all-atom simulations, noticeable advances have recently been achieved, mainly concerning the use of more rigorous parameterization techniques and novel algorithms for sampling configurational space. Moreover, the simulation size scales and timescales coincide with those that can be reached with the most advanced spectroscopic techniques, making it possible to directly compare simulation and experiment.
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            Linear Scaling Density Functional Calculations with Gaussian Orbitals

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              Coarse-grained models of protein folding: toy models or predictive tools?

              Coarse-grained models are emerging as a practical alternative to all-atom simulations for the characterization of protein folding mechanisms over long time scales. While a decade ago minimalist toy models were mainly designed to test general hypotheses on the principles regulating protein folding, the latest coarse-grained models are increasingly realistic and can be used to characterize quantitatively the detailed folding mechanism of specific proteins. The ability of such models to reproduce the essential features of folding dynamics suggests that each single atomic degree of freedom is not by itself particularly relevant to folding and supports a statistical mechanical approach to characterize folding transitions. When combined with more refined models and with experimental studies, the systematic investigation of protein systems and complexes using coarse-grained models can advance our theoretical understanding of the actual organizing principles that emerge from the complex network of interactions among protein atomic constituents.
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                Author and article information

                Contributors
                Journal
                AIMS Biophysics
                AIMS Biophysics
                AIMS Press
                2377-9098
                13 March 2014
                : 1
                : 1
                : 1-15
                Affiliations
                [1 ] Department of Cardiovascular Physiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan;
                [2 ] School of Medicine, Okayama University, Okayama, Japan
                Author notes
                Ken Takahashi,E-mail: takah-k2@ 123456okayama-u.ac.jp ; Tel: +81-86-235-7119
                Article
                10.3934/biophy.2014.1.1
                617cb9cb-1991-46a9-921e-56b454a637ff
                History
                : 23 December 2013
                : 28 February 2014
                Categories
                Review

                Biophysics
                coarse-grained molecular dynamics,all atom-molecular dynamics,reverse graining,protein-protein interactions,protein-lipid interactions,in silico drug design

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