Relaxation mode analysis for molecular dynamics simulations of proteins
Molecular dynamics simulation is a powerful method for investigating the structural stability, dynamics, and function of biopolymers at the atomic level. In recent years, it has become possible to perform simulations on time scales of the order of milliseconds using special hardware. However, it is...
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Published in | Biophysical reviews Vol. 10; no. 2; pp. 375 - 389 |
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Main Authors | , |
Format | Journal Article |
Language | English |
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Berlin/Heidelberg
Springer Berlin Heidelberg
01.04.2018
Springer Nature B.V |
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Abstract | Molecular dynamics simulation is a powerful method for investigating the structural stability, dynamics, and function of biopolymers at the atomic level. In recent years, it has become possible to perform simulations on time scales of the order of milliseconds using special hardware. However, it is necessary to derive the important factors contributing to structural change or function from the complicated movements of biopolymers obtained from long simulations. Although some analysis methods for protein systems have been developed using increasing simulation times, many of these methods are static in nature (i.e., no information on time). In recent years, dynamic analysis methods have been developed, such as the Markov state model and relaxation mode analysis (RMA), which was introduced based on spin and homopolymer systems. The RMA method approximately extracts slow relaxation modes and rates from trajectories and decomposes the structural fluctuations into slow relaxation modes, which characterize the slow relaxation dynamics of the system. Recently, this method has been applied to biomolecular systems. In this article, we review RMA and its improved versions for protein systems. |
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AbstractList | Molecular dynamics simulation is a powerful method for investigating the structural stability, dynamics, and function of biopolymers at the atomic level. In recent years, it has become possible to perform simulations on time scales of the order of milliseconds using special hardware. However, it is necessary to derive the important factors contributing to structural change or function from the complicated movements of biopolymers obtained from long simulations. Although some analysis methods for protein systems have been developed using increasing simulation times, many of these methods are static in nature (i.e., no information on time). In recent years, dynamic analysis methods have been developed, such as the Markov state model and relaxation mode analysis (RMA), which was introduced based on spin and homopolymer systems. The RMA method approximately extracts slow relaxation modes and rates from trajectories and decomposes the structural fluctuations into slow relaxation modes, which characterize the slow relaxation dynamics of the system. Recently, this method has been applied to biomolecular systems. In this article, we review RMA and its improved versions for protein systems. |
Author | Mitsutake, Ayori Takano, Hiroshi |
Author_xml | – sequence: 1 givenname: Ayori surname: Mitsutake fullname: Mitsutake, Ayori email: ayori@mail.rk.phys.keio.ac.jp organization: Department of Physics, Faculty of Science and Technology, Keio University – sequence: 2 givenname: Hiroshi surname: Takano fullname: Takano, Hiroshi organization: Department of Physics, Faculty of Science and Technology, Keio University |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29546562$$D View this record in MEDLINE/PubMed |
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Keywords | Simulation Dynamics Analysis Protein |
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Snippet | Molecular dynamics simulation is a powerful method for investigating the structural stability, dynamics, and function of biopolymers at the atomic level. In... |
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SubjectTerms | Atomic structure Biochemistry Biological and Medical Physics Biological Techniques Biomedical and Life Sciences Biophysics Biopolymers Cell Biology Computer simulation Dynamic stability Dynamic structural analysis Life Sciences Markov chains Membrane Biology Methods Molecular dynamics Nanotechnology Proteins Review Simulation Structural stability Variations |
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Title | Relaxation mode analysis for molecular dynamics simulations of proteins |
URI | https://link.springer.com/article/10.1007/s12551-018-0406-7 https://www.ncbi.nlm.nih.gov/pubmed/29546562 https://www.proquest.com/docview/2024991212/abstract/ https://search.proquest.com/docview/2014948749 https://pubmed.ncbi.nlm.nih.gov/PMC5899748 |
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