A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes

D. Vijay Anand; Zhenyu Meng; Kelin Xia

doi:10.1039/c8cp07442a

A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes

Physical Chemistry Chemical Physics ◽

10.1039/c8cp07442a ◽

2019 ◽

Vol 21 (8) ◽

pp. 4359-4366 ◽

Cited By ~ 1

Author(s):

D. Vijay Anand ◽

Zhenyu Meng ◽

Kelin Xia

Keyword(s):

Normal Mode ◽

Network Model ◽

Material Properties ◽

Normal Mode Analysis ◽

Mode Analysis ◽

Particle Model ◽

Elastic Network Model ◽

Elastic Network ◽

Virtual Particle ◽

Biomolecular Complexes

The CMVP-ENM for virus normal mode analysis. With a special ratio parameter, CMVP-ENM can characterize the multi-material properties of biomolecular complexes and systematically enhance or suppress the modes for different components.

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Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules

Physical Chemistry Chemical Physics ◽

10.1039/c7cp07177a ◽

2018 ◽

Vol 20 (1) ◽

pp. 658-669 ◽

Cited By ~ 7

Author(s):

Kelin Xia

Keyword(s):

Normal Mode ◽

Network Model ◽

Normal Mode Analysis ◽

Mode Analysis ◽

Elastic Network Model ◽

Elastic Network ◽

Virtual Particle

In this paper, a multiscale virtual particle based elastic network model (MVP-ENM) is proposed for the normal mode analysis of large-sized biomolecules.

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Simplified Normal Mode Analysis of Conformational Transitions in DNA-dependent Polymerases: the Elastic Network Model

Journal of Molecular Biology ◽

10.1016/s0022-2836(02)00562-4 ◽

2002 ◽

Vol 320 (5) ◽

pp. 1011-1024 ◽

Cited By ~ 188

Author(s):

M Delarue ◽

Y.-H Sanejouand

Keyword(s):

Normal Mode ◽

Network Model ◽

Normal Mode Analysis ◽

Conformational Transitions ◽

Mode Analysis ◽

Elastic Network Model ◽

Elastic Network

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Comparison of all-atom and coarse-grained normal mode analysis in the elastic network model

Journal of Mechanical Science and Technology ◽

10.1007/s12206-013-0849-5 ◽

2013 ◽

Vol 27 (11) ◽

pp. 3267-3275 ◽

Cited By ~ 1

Author(s):

Ming-Wen Hu ◽

Brian O’Riordan ◽

Byung Kim ◽

Moon Ki Kim

Keyword(s):

Normal Mode ◽

Network Model ◽

Normal Mode Analysis ◽

Coarse Grained ◽

Mode Analysis ◽

Elastic Network Model ◽

Elastic Network

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Precise Normal Mode Analysis and Frequency Prediction of DNA Nanostructure through Mass-Weighted Chemical Elastic Network Model

Biophysical Journal ◽

10.1016/j.bpj.2012.11.2786 ◽

2013 ◽

Vol 104 (2) ◽

pp. 505a

Author(s):

Soojin Jo ◽

Min Hyeok Kim ◽

Junyoung Son ◽

Sung Ha Park ◽

Moon Ki Kim

Keyword(s):

Normal Mode ◽

Network Model ◽

Normal Mode Analysis ◽

Mode Analysis ◽

Elastic Network Model ◽

Elastic Network ◽

Dna Nanostructure

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Elastic network model-based normal mode analysis reveals the conformational couplings in the tripartite AcrAB-TolC multidrug efflux complex

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.23143 ◽

2011 ◽

Vol 79 (10) ◽

pp. 2936-2945 ◽

Cited By ~ 9

Author(s):

Beibei Wang ◽

Jingwei Weng ◽

Kangnian Fan ◽

Wenning Wang

Keyword(s):

Normal Mode ◽

Network Model ◽

Normal Mode Analysis ◽

Mode Analysis ◽

Elastic Network Model ◽

Multidrug Efflux ◽

Elastic Network ◽

Model Based

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1P-083 Assessment of normal mode analysis with an elastic network model in dihedral angle space(The 46th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.48.s34_1 ◽

2008 ◽

Vol 48 (supplement) ◽

pp. S34

Author(s):

Hiroshi Wako ◽

Shigeru Endo

Keyword(s):

Annual Meeting ◽

Dihedral Angle ◽

Normal Mode ◽

Network Model ◽

Normal Mode Analysis ◽

Mode Analysis ◽

Elastic Network Model ◽

Elastic Network ◽

Biophysical Society ◽

Angle Space

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Identification of Dynamical Correlations within the Myosin Motor Domain by the Normal Mode Analysis of an Elastic Network Model

Journal of Molecular Biology ◽

10.1016/j.jmb.2004.12.020 ◽

2005 ◽

Vol 346 (3) ◽

pp. 745-759 ◽

Cited By ~ 88

Author(s):

Wenjun Zheng ◽

Bernard Brooks

Keyword(s):

Normal Mode ◽

Network Model ◽

Normal Mode Analysis ◽

Motor Domain ◽

Mode Analysis ◽

Elastic Network Model ◽

Elastic Network ◽

Myosin Motor ◽

Myosin Motor Domain

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Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables

Computational Biology and Chemistry ◽

10.1016/j.compbiolchem.2013.02.006 ◽

2013 ◽

Vol 44 ◽

pp. 22-30 ◽

Cited By ~ 18

Author(s):

Hiroshi Wako ◽

Shigeru Endo

Keyword(s):

Protein Data Bank ◽

Normal Mode ◽

Network Model ◽

Normal Mode Analysis ◽

Data Bank ◽

Mode Analysis ◽

Dihedral Angles ◽

Elastic Network Model ◽

Elastic Network ◽

Independent Variables

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Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

Biophysical Journal ◽

10.1016/j.bpj.2010.03.027 ◽

2010 ◽

Vol 98 (12) ◽

pp. 3025-3034 ◽

Cited By ~ 24

Author(s):

Wenjun Zheng

Keyword(s):

Crystal Structures ◽

Normal Mode ◽

Network Model ◽

Normal Mode Analysis ◽

Protein Crystal ◽

Mode Analysis ◽

Elastic Network Model ◽

Elastic Network

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Geometrical Conversion of the EGFR Extracellular Domain by Adiabatic Mapping Combining Normal Mode Analysis of the Elastic Network Model and Energy Optimization

Chemical and Pharmaceutical Bulletin ◽

10.1248/cpb.c19-00205 ◽

2019 ◽

Vol 67 (10) ◽

pp. 1061-1071

Author(s):

Hiroyuki Nojima ◽

Yasuomi Kiyota ◽

Genki Terashi ◽

Mayuko Takeda-Shitaka ◽

Hajime Matsubara

Keyword(s):

Normal Mode ◽

Network Model ◽

Normal Mode Analysis ◽

Energy Optimization ◽

Extracellular Domain ◽

Mode Analysis ◽

Elastic Network Model ◽

Elastic Network

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