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Molecular dynamics simulation in virus research

Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how the...

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Detalles Bibliográficos
Autores principales: Ode, Hirotaka, Nakashima, Masaaki, Kitamura, Shingo, Sugiura, Wataru, Sato, Hironori
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400276/
https://www.ncbi.nlm.nih.gov/pubmed/22833741
http://dx.doi.org/10.3389/fmicb.2012.00258
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author Ode, Hirotaka
Nakashima, Masaaki
Kitamura, Shingo
Sugiura, Wataru
Sato, Hironori
author_facet Ode, Hirotaka
Nakashima, Masaaki
Kitamura, Shingo
Sugiura, Wataru
Sato, Hironori
author_sort Ode, Hirotaka
collection PubMed
description Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Molecular dynamics (MD) simulation is a powerful computational method for delineating motions of proteins at an atomic-scale via theoretical and empirical principles in physical chemistry. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. Consequently, MD simulation is quickly extending the range of applications in biology, helping to reveal unique features of protein structures that would be hard to obtain by experimental methods alone. In this review, we summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique.
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spelling pubmed-34002762012-07-25 Molecular dynamics simulation in virus research Ode, Hirotaka Nakashima, Masaaki Kitamura, Shingo Sugiura, Wataru Sato, Hironori Front Microbiol Microbiology Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Molecular dynamics (MD) simulation is a powerful computational method for delineating motions of proteins at an atomic-scale via theoretical and empirical principles in physical chemistry. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. Consequently, MD simulation is quickly extending the range of applications in biology, helping to reveal unique features of protein structures that would be hard to obtain by experimental methods alone. In this review, we summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique. Frontiers Media S.A. 2012-07-19 /pmc/articles/PMC3400276/ /pubmed/22833741 http://dx.doi.org/10.3389/fmicb.2012.00258 Text en Copyright © 2012 Ode, Nakashima, Kitamura, Sugiura and Sato. http://www.frontiersin.org/licenseagreement This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.
spellingShingle Microbiology
Ode, Hirotaka
Nakashima, Masaaki
Kitamura, Shingo
Sugiura, Wataru
Sato, Hironori
Molecular dynamics simulation in virus research
title Molecular dynamics simulation in virus research
title_full Molecular dynamics simulation in virus research
title_fullStr Molecular dynamics simulation in virus research
title_full_unstemmed Molecular dynamics simulation in virus research
title_short Molecular dynamics simulation in virus research
title_sort molecular dynamics simulation in virus research
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400276/
https://www.ncbi.nlm.nih.gov/pubmed/22833741
http://dx.doi.org/10.3389/fmicb.2012.00258
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