Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis

Alexandros Altis; Moritz Otten; Phuong H. Nguyen; Rainer Hegger; Gerhard Stock

doi:10.1063/1.2945165

Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis

The Journal of Chemical Physics ◽

10.1063/1.2945165 ◽

2008 ◽

Vol 128 (24) ◽

pp. 245102 ◽

Cited By ~ 90

Author(s):

Alexandros Altis ◽

Moritz Otten ◽

Phuong H. Nguyen ◽

Rainer Hegger ◽

Gerhard Stock

Keyword(s):

Principal Component Analysis ◽

Free Energy ◽

Dihedral Angle ◽

Energy Landscape ◽

Principal Component ◽

Component Analysis ◽

Free Energy Landscape

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Free-Energy Landscape of RNA Hairpins Constructed via Dihedral Angle Principal Component Analysis

The Journal of Physical Chemistry B ◽

10.1021/jp9076036 ◽

2009 ◽

Vol 113 (52) ◽

pp. 16660-16668 ◽

Cited By ~ 36

Author(s):

Laura Riccardi ◽

Phuong H. Nguyen ◽

Gerhard Stock

Keyword(s):

Principal Component Analysis ◽

Free Energy ◽

Dihedral Angle ◽

Energy Landscape ◽

Principal Component ◽

Component Analysis ◽

Free Energy Landscape ◽

Rna Hairpins

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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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Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics

The Journal of Chemical Physics ◽

10.1063/1.4810884 ◽

2013 ◽

Vol 138 (23) ◽

pp. 235101 ◽

Cited By ~ 17

Author(s):

François Sicard ◽

Patrick Senet

Keyword(s):

Principal Component Analysis ◽

Free Energy ◽

Energy Landscape ◽

Principal Component ◽

Component Analysis ◽

Free Energy Landscape

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Energy landscape of a small peptide revealed by dihedral angle principal component analysis

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20310 ◽

2004 ◽

Vol 58 (1) ◽

pp. 45-52 ◽

Cited By ~ 258

Author(s):

Yuguang Mu ◽

Phuong H. Nguyen ◽

Gerhard Stock

Keyword(s):

Principal Component Analysis ◽

Dihedral Angle ◽

Energy Landscape ◽

Principal Component ◽

Component Analysis ◽

Small Peptide

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Comment on: “Energy landscape of a small peptide revealed by dihedral angle principal component analysis”

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20900 ◽

2006 ◽

Vol 64 (3) ◽

pp. 795-797 ◽

Cited By ~ 13

Author(s):

Konrad Hinsen

Keyword(s):

Principal Component Analysis ◽

Dihedral Angle ◽

Energy Landscape ◽

Principal Component ◽

Component Analysis ◽

Small Peptide

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Reply to the comment on “Energy landscape of a small peptide revealed by dihedral angle principal component analysis”

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21038 ◽

2006 ◽

Vol 64 (3) ◽

pp. 798-799 ◽

Cited By ~ 8

Author(s):

Yuguang Mu ◽

Phuong Nguyen ◽

Gerhard Stock

Keyword(s):

Principal Component Analysis ◽

Dihedral Angle ◽

Energy Landscape ◽

Principal Component ◽

Component Analysis ◽

Small Peptide

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Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21185 ◽

2006 ◽

Vol 65 (4) ◽

pp. 898-913 ◽

Cited By ~ 23

Author(s):

Phuong H. Nguyen

Keyword(s):

Principal Component Analysis ◽

Free Energy ◽

Principal Component ◽

Component Analysis ◽

Energy Landscapes ◽

Nonlinear Principal Component Analysis ◽

Free Energy Landscapes

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Hidden Complexity of Protein Free-Energy Landscapes Revealed by Principal Component Analysis by Parts

The Journal of Physical Chemistry Letters ◽

10.1021/jz101069e ◽

2010 ◽

Vol 1 (19) ◽

pp. 2769-2773 ◽

Cited By ~ 20

Author(s):

Abhinav Jain ◽

Rainer Hegger ◽

Gerhard Stock

Keyword(s):

Principal Component Analysis ◽

Free Energy ◽

Principal Component ◽

Component Analysis ◽

Energy Landscapes ◽

Free Energy Landscapes

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3TA1-03 Principal Component Analysis of Proteins in Dihedral Angle Space(The 47th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.49.s51_6 ◽

2009 ◽

Vol 49 (supplement) ◽

pp. S51-S52

Author(s):

Satoshi Omori ◽

Sotaro Fuchigami ◽

Mitsunori Ikeguchi ◽

Akinori Kidera

Keyword(s):

Principal Component Analysis ◽

Annual Meeting ◽

Dihedral Angle ◽

Principal Component ◽

Component Analysis ◽

Biophysical Society ◽

Angle Space

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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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