Coarse-grained molecular dynamics simulations of biomolecules
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 simi...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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AIMS Press
2014-03-01
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| Series: | AIMS Biophysics |
| Subjects: | |
| Online Access: | http://www.aimspress.com/biophysics/article/161/fulltext.html |
| _version_ | 1828367860015038464 |
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| author | Ken Takahashi Takayuki Oda Keiji Naruse |
| author_facet | Ken Takahashi Takayuki Oda Keiji Naruse |
| author_sort | Ken Takahashi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-14T06:03:51Z |
| format | Article |
| id | doaj.art-9b09fb2e87184e17a2b3e5ea7c93ccc3 |
| institution | Directory Open Access Journal |
| issn | 2377-9098 |
| language | English |
| last_indexed | 2024-04-14T06:03:51Z |
| publishDate | 2014-03-01 |
| publisher | AIMS Press |
| record_format | Article |
| series | AIMS Biophysics |
| spelling | doaj.art-9b09fb2e87184e17a2b3e5ea7c93ccc32022-12-22T02:08:39ZengAIMS PressAIMS Biophysics2377-90982014-03-011111510.3934/biophy.2014.1.120140101Coarse-grained molecular dynamics simulations of biomoleculesKen Takahashi0Takayuki Oda1Keiji Naruse2Department of Cardiovascular Physiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, JapanSchool of Medicine, Okayama University, Okayama, JapaDepartment of Cardiovascular Physiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, JapanCoarse-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.http://www.aimspress.com/biophysics/article/161/fulltext.htmlcoarse-grained molecular dynamicsall atom-molecular dynamicsreverse grainingprotein-protein interactionsprotein-lipid interactionsin silico drug design |
| spellingShingle | Ken Takahashi Takayuki Oda Keiji Naruse Coarse-grained molecular dynamics simulations of biomolecules AIMS Biophysics coarse-grained molecular dynamics all atom-molecular dynamics reverse graining protein-protein interactions protein-lipid interactions in silico drug design |
| title | Coarse-grained molecular dynamics simulations of biomolecules |
| title_full | Coarse-grained molecular dynamics simulations of biomolecules |
| title_fullStr | Coarse-grained molecular dynamics simulations of biomolecules |
| title_full_unstemmed | Coarse-grained molecular dynamics simulations of biomolecules |
| title_short | Coarse-grained molecular dynamics simulations of biomolecules |
| title_sort | coarse grained molecular dynamics simulations of biomolecules |
| topic | coarse-grained molecular dynamics all atom-molecular dynamics reverse graining protein-protein interactions protein-lipid interactions in silico drug design |
| url | http://www.aimspress.com/biophysics/article/161/fulltext.html |
| work_keys_str_mv | AT kentakahashi coarsegrainedmoleculardynamicssimulationsofbiomolecules AT takayukioda coarsegrainedmoleculardynamicssimulationsofbiomolecules AT keijinaruse coarsegrainedmoleculardynamicssimulationsofbiomolecules |