Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics

Molecular dynamics (MD) techniques enable atomic-level observations, but simulations of “slow” biomolecular processes are challenging because of current computer speed limitations. Here, the authors develop a method to accelerate MD simulations by high-frequency ultrasound perturbation and reveal bi...

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Autores principales:	Mitsugu Araki, Shigeyuki Matsumoto, Gert-Jan Bekker, Yuta Isaka, Yukari Sagae, Narutoshi Kamiya, Yasushi Okuno
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Science Q
Acceso en línea:	https://doaj.org/article/948c894a587d4e55a4cd9da8f1b04294
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spelling	oai:doaj.org-article:948c894a587d4e55a4cd9da8f1b042942021-12-02T16:50:35ZExploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics10.1038/s41467-021-23157-12041-1723https://doaj.org/article/948c894a587d4e55a4cd9da8f1b042942021-05-01T00:00:00Zhttps://doi.org/10.1038/s41467-021-23157-1https://doaj.org/toc/2041-1723Molecular dynamics (MD) techniques enable atomic-level observations, but simulations of “slow” biomolecular processes are challenging because of current computer speed limitations. Here, the authors develop a method to accelerate MD simulations by high-frequency ultrasound perturbation and reveal binding events between the protein CDK2 and its small-molecule inhibitors.Mitsugu ArakiShigeyuki MatsumotoGert-Jan BekkerYuta IsakaYukari SagaeNarutoshi KamiyaYasushi OkunoNature PortfolioarticleScienceQENNature Communications, Vol 12, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Science Q
spellingShingle	Science Q Mitsugu Araki Shigeyuki Matsumoto Gert-Jan Bekker Yuta Isaka Yukari Sagae Narutoshi Kamiya Yasushi Okuno Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics
description	Molecular dynamics (MD) techniques enable atomic-level observations, but simulations of “slow” biomolecular processes are challenging because of current computer speed limitations. Here, the authors develop a method to accelerate MD simulations by high-frequency ultrasound perturbation and reveal binding events between the protein CDK2 and its small-molecule inhibitors.
format	article
author	Mitsugu Araki Shigeyuki Matsumoto Gert-Jan Bekker Yuta Isaka Yukari Sagae Narutoshi Kamiya Yasushi Okuno
author_facet	Mitsugu Araki Shigeyuki Matsumoto Gert-Jan Bekker Yuta Isaka Yukari Sagae Narutoshi Kamiya Yasushi Okuno
author_sort	Mitsugu Araki
title	Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics
title_short	Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics
title_full	Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics
title_fullStr	Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics
title_full_unstemmed	Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics
title_sort	exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/948c894a587d4e55a4cd9da8f1b04294
work_keys_str_mv	AT mitsuguaraki exploringligandbindingpathwaysonproteinsusinghypersoundacceleratedmoleculardynamics AT shigeyukimatsumoto exploringligandbindingpathwaysonproteinsusinghypersoundacceleratedmoleculardynamics AT gertjanbekker exploringligandbindingpathwaysonproteinsusinghypersoundacceleratedmoleculardynamics AT yutaisaka exploringligandbindingpathwaysonproteinsusinghypersoundacceleratedmoleculardynamics AT yukarisagae exploringligandbindingpathwaysonproteinsusinghypersoundacceleratedmoleculardynamics AT narutoshikamiya exploringligandbindingpathwaysonproteinsusinghypersoundacceleratedmoleculardynamics AT yasushiokuno exploringligandbindingpathwaysonproteinsusinghypersoundacceleratedmoleculardynamics
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Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics

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