Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions

M. Gur; E. Zomot; I. Bahar

doi:10.1063/1.4816375

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions

The Journal of Chemical Physics ◽

10.1063/1.4816375 ◽

2013 ◽

Vol 139 (12) ◽

pp. 121912 ◽

Cited By ~ 52

Author(s):

M. Gur ◽

E. Zomot ◽

I. Bahar

Keyword(s):

Network Model ◽

Model Predictions ◽

Anisotropic Network ◽

Anisotropic Network Model

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Correction: Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

PLoS Computational Biology ◽

10.1371/journal.pcbi.1003868 ◽

2014 ◽

Vol 10 (8) ◽

pp. e1003868

Author(s):

Keyword(s):

Network Model ◽

Conformational Transitions ◽

Biomolecular Systems ◽

Anisotropic Network ◽

Anisotropic Network Model

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Anisotropic network model: systematic evaluation and a new web interface

Bioinformatics ◽

10.1093/bioinformatics/btl448 ◽

2006 ◽

Vol 22 (21) ◽

pp. 2619-2627 ◽

Cited By ~ 213

Author(s):

E. Eyal ◽

L.-W. Yang ◽

I. Bahar

Keyword(s):

Network Model ◽

Systematic Evaluation ◽

Web Interface ◽

Anisotropic Network ◽

Anisotropic Network Model

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Exact Expressions for Many-Body Atomic Displacement Correlations in the Anisotropic Network Model

Biophysical Journal ◽

10.1016/j.bpj.2011.11.2442 ◽

2012 ◽

Vol 102 (3) ◽

pp. 445a-446a

Author(s):

Osman B. Okan ◽

Aravind Rammohan ◽

Rahmi Ozisik

Keyword(s):

Network Model ◽

Atomic Displacement ◽

Many Body ◽

Anisotropic Network ◽

Anisotropic Network Model

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Tensorial elastic network model for protein dynamics: Integration of the anisotropic network model with bond-bending and twist elasticities

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24153 ◽

2012 ◽

Vol 80 (12) ◽

pp. 2692-2700 ◽

Cited By ~ 9

Author(s):

Amit Srivastava ◽

Roee Ben Halevi ◽

Alexander Veksler ◽

Rony Granek

Keyword(s):

Protein Dynamics ◽

Network Model ◽

Elastic Network Model ◽

Elastic Network ◽

Bond Bending ◽

Anisotropic Network ◽

Anisotropic Network Model

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Stiffening of flexible SUMO1 protein upon peptide-binding: Analysis with anisotropic network model

Mathematical Biosciences ◽

10.1016/j.mbs.2017.11.008 ◽

2018 ◽

Vol 295 ◽

pp. 67-72 ◽

Cited By ~ 4

Author(s):

Ranja Sarkar

Keyword(s):

Network Model ◽

Peptide Binding ◽

Binding Analysis ◽

Anisotropic Network ◽

Anisotropic Network Model

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Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

PLoS Computational Biology ◽

10.1371/journal.pcbi.1003521 ◽

2014 ◽

Vol 10 (4) ◽

pp. e1003521 ◽

Cited By ~ 83

Author(s):

Avisek Das ◽

Mert Gur ◽

Mary Hongying Cheng ◽

Sunhwan Jo ◽

Ivet Bahar ◽

...

Keyword(s):

Network Model ◽

Conformational Transitions ◽

Biomolecular Systems ◽

Anisotropic Network ◽

Anisotropic Network Model

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Targeted Conformational Transitions of Multimeric Proteins by Monte Carlo Simulations Combined with Collective Anisotropic Network Model Modes

Biophysical Journal ◽

10.1016/j.bpj.2014.11.1169 ◽

2015 ◽

Vol 108 (2) ◽

pp. 211a

Author(s):

Yasemin Yesiltepe ◽

Arzu Uyar ◽

Deniz Turgut ◽

Turkan Haliloglu ◽

Pemra Doruker ◽

...

Keyword(s):

Monte Carlo ◽

Monte Carlo Simulations ◽

Network Model ◽

Conformational Transitions ◽

Anisotropic Network ◽

Anisotropic Network Model

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Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM)

The Journal of Chemical Physics ◽

10.1063/1.4936132 ◽

2015 ◽

Vol 143 (20) ◽

pp. 204106 ◽

Cited By ~ 18

Author(s):

Kelin Xia ◽

Kristopher Opron ◽

Guo-Wei Wei

Keyword(s):

Network Model ◽

Gaussian Network Model ◽

Anisotropic Network ◽

Gaussian Network ◽

Anisotropic Network Model

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Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network model

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2020.107778 ◽

2021 ◽

Vol 102 ◽

pp. 107778

Author(s):

Satyabrata Majumder ◽

Dwaipayan Chaudhuri ◽

Joyeeta Datta ◽

Kalyan Giri

Keyword(s):

Normal Mode ◽

Network Model ◽

Normal Mode Analysis ◽

Mode Analysis ◽

Spike Glycoprotein ◽

Anisotropic Network ◽

Anisotropic Network Model

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Augmenting the anisotropic network model with torsional potentials improves PATH performance, enabling detailed comparison with experimental rate data

Structural Dynamics ◽

10.1063/1.4976142 ◽

2017 ◽

Vol 4 (3) ◽

pp. 032103 ◽

Cited By ~ 5

Author(s):

Srinivas Niranj Chandrasekaran ◽

Charles W. Carter

Keyword(s):

Network Model ◽

Detailed Comparison ◽

Rate Data ◽

Experimental Rate ◽

Anisotropic Network ◽

Torsional Potentials ◽

Anisotropic Network Model

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