Principal component analysis of nonequilibrium molecular dynamics simulations

Matthias Post; Steffen Wolf; Gerhard Stock

doi:10.1063/1.5089636

Principal component analysis of nonequilibrium molecular dynamics simulations

The Journal of Chemical Physics ◽

10.1063/1.5089636 ◽

2019 ◽

Vol 150 (20) ◽

pp. 204110 ◽

Cited By ~ 6

Author(s):

Matthias Post ◽

Steffen Wolf ◽

Gerhard Stock

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Molecular Dynamics Simulations ◽

Principal Component ◽

Component Analysis ◽

Nonequilibrium Molecular Dynamics ◽

Dynamics Simulations

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Faculty Opinions recommendation of Principal component analysis of nonequilibrium molecular dynamics simulations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.735899830.793561013 ◽

2019 ◽

Author(s):

Jeremy C Smith

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Molecular Dynamics Simulations ◽

Principal Component ◽

Component Analysis ◽

Nonequilibrium Molecular Dynamics ◽

Dynamics Simulations

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Molecular mechanism concerning conformational changes of CDK2 mediated by binding of inhibitors using molecular dynamics simulations and principal component analysis

SAR and QSAR in Environmental Research ◽

10.1080/1062936x.2021.1934896 ◽

2021 ◽

pp. 1-22

Author(s):

S.S. Liang ◽

X.G. Liu ◽

Y.X. Cui ◽

S.L. Zhang ◽

Q.G. Zhang ◽

...

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Molecular Dynamics Simulations ◽

Molecular Mechanism ◽

Conformational Changes ◽

Principal Component ◽

Component Analysis ◽

Dynamics Simulations

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Insights in the structural understanding of amyloidogenicity and mutation-led conformational dynamics of amyloid beta (Aβ) through molecular dynamics simulations and principal component analysis

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2021.1871955 ◽

2021 ◽

pp. 1-11

Author(s):

Sriram Srinivasa Raghavan ◽

Saleem Iqbal ◽

Niraikulam Ayyadurai ◽

Krishnasamy Gunasekaran

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Molecular Dynamics Simulations ◽

Amyloid Beta ◽

Conformational Dynamics ◽

Principal Component ◽

Component Analysis ◽

Dynamics Simulations

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Molecular Dynamics Simulations and Principal Component Analysis on Human Laforin Mutation W32G and W32G/K87A

The Protein Journal ◽

10.1007/s10930-014-9561-2 ◽

2014 ◽

Vol 33 (3) ◽

pp. 289-295 ◽

Cited By ~ 15

Author(s):

P. S. Srikumar ◽

K. Rohini ◽

Perumbilavil Kaithamanakallam Rajesh

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Molecular Dynamics Simulations ◽

Principal Component ◽

Component Analysis ◽

Dynamics Simulations

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Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.5b01106 ◽

2016 ◽

Vol 12 (3) ◽

pp. 1019-1028 ◽

Cited By ~ 9

Author(s):

Pavel Buslaev ◽

Valentin Gordeliy ◽

Sergei Grudinin ◽

Ivan Gushchin

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Molecular Dynamics Simulations ◽

Conformational Changes ◽

Principal Component ◽

Component Analysis ◽

Lipid Molecule ◽

Dynamics Simulations

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Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2019.07.008 ◽

2019 ◽

Vol 92 ◽

pp. 112-122 ◽

Cited By ~ 3

Author(s):

Konda Reddy Karnati ◽

Yixuan Wang

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Binding Free Energy ◽

Principal Component ◽

Component Analysis ◽

Ligand Interactions ◽

Dynamics Simulations ◽

Hiv 1

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Functional roles of magnesium binding to extracellular signal-regulated kinase 2 explored by molecular dynamics simulations and principal component analysis

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2016.1277783 ◽

2017 ◽

Vol 36 (2) ◽

pp. 351-361 ◽

Cited By ~ 14

Author(s):

Jianzhong Chen

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Molecular Dynamics Simulations ◽

Principal Component ◽

Component Analysis ◽

Functional Roles ◽

Extracellular Signal Regulated Kinase ◽

Magnesium Binding ◽

Extracellular Signal ◽

Dynamics Simulations

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Conformational transformation of switch domains in GDP/K-Ras induced by G13 mutants: an investigation through Gaussian accelerated molecular dynamics simulations and principal component analysis

Computers in Biology and Medicine ◽

10.1016/j.compbiomed.2021.104639 ◽

2021 ◽

pp. 104639

Author(s):

Jianzhong Chen ◽

Lifei Wang ◽

Wei Wang ◽

Haibo Sun ◽

Laixue Pang ◽

...

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Molecular Dynamics Simulations ◽

Principal Component ◽

Component Analysis ◽

Conformational Transformation ◽

Accelerated Molecular Dynamics ◽

Dynamics Simulations

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Probing molecular mechanism of inhibitor bindings to bromodomain-containing protein 4 based on molecular dynamics simulations and principal component analysis

SAR and QSAR in Environmental Research ◽

10.1080/1062936x.2020.1777584 ◽

2020 ◽

Vol 31 (7) ◽

pp. 547-570

Author(s):

S.L. Wu ◽

L.F. Wang ◽

H.B. Sun ◽

W. Wang ◽

Y.X. Yu

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Molecular Dynamics Simulations ◽

Molecular Mechanism ◽

Principal Component ◽

Component Analysis ◽

Dynamics Simulations

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Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2009.01.006 ◽

2009 ◽

Vol 27 (8) ◽

pp. 889-899 ◽

Cited By ~ 114

Author(s):

Elena Papaleo ◽

Paolo Mereghetti ◽

Piercarlo Fantucci ◽

Rita Grandori ◽

Luca De Gioia

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Energy Landscape ◽

Principal Component ◽

Component Analysis ◽

Free Energy Landscape ◽

Structural Clustering ◽

Dynamics Simulations

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