Molecular Dynamics Simulations of the Chromophore Binding Site ofDeinococcus radioduransBacteriophytochrome Using New Force Field Parameters for the Phytochromobilin Chromophore

Steve Kaminski; Grazia Daminelli; Maria Andrea Mroginski

doi:10.1021/jp8047532

Molecular Dynamics Simulations of the Chromophore Binding Site ofDeinococcus radioduransBacteriophytochrome Using New Force Field Parameters for the Phytochromobilin Chromophore

The Journal of Physical Chemistry B ◽

10.1021/jp8047532 ◽

2009 ◽

Vol 113 (4) ◽

pp. 945-958 ◽

Cited By ~ 21

Author(s):

Steve Kaminski ◽

Grazia Daminelli ◽

Maria Andrea Mroginski

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Binding Site ◽

Force Field Parameters ◽

Dynamics Simulations

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New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations

RSC Advances ◽

10.1039/c4ra09897h ◽

2014 ◽

Vol 4 (89) ◽

pp. 48621-48631 ◽

Cited By ~ 9

Author(s):

Eleanor R. Turpin ◽

Sam Mulholland ◽

Andrew M. Teale ◽

Boyan B. Bonev ◽

Jonathan D. Hirst

Keyword(s):

Molecular Dynamics ◽

Amino Acid ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Amino Acid Residues ◽

Charmm Force Field ◽

Force Field Parameters ◽

Dynamics Simulations

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A test of improved force field parameters for urea: molecular-dynamics simulations of urea crystals

Journal of Molecular Modeling ◽

10.1007/s00894-011-1336-5 ◽

2012 ◽

Vol 18 (8) ◽

pp. 3455-3466 ◽

Cited By ~ 5

Author(s):

Gül Altınbaş Özpınar ◽

Frank R. Beierlein ◽

Wolfgang Peukert ◽

Dirk Zahn ◽

Timothy Clark

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Force Field Parameters ◽

Dynamics Simulations

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Back Cover: Ab initio derived force-field parameters for molecular dynamics simulations of deprotonated amorphous-SiO2 /water interfaces (Phys. Status Solidi B 2/2012)

physica status solidi (b) ◽

10.1002/pssb.201290001 ◽

2012 ◽

Vol 249 (2) ◽

Author(s):

Anke Butenuth ◽

Gianpietro Moras ◽

Julian Schneider ◽

Mohammad Koleini ◽

Susan Köppen ◽

...

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Amorphous Sio2 ◽

Back Cover ◽

Force Field Parameters ◽

Dynamics Simulations

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Molecular Dynamics Simulations Based on Newly Developed Force Field Parameters for Cu2+ Spin Labels Provide Insights into Double-Histidine-Based Double Electron–Electron Resonance

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.0c00739 ◽

2020 ◽

Vol 124 (14) ◽

pp. 2788-2797 ◽

Cited By ~ 10

Author(s):

Xiaowei Bogetti ◽

Shreya Ghosh ◽

Austin Gamble Jarvi ◽

Junmei Wang ◽

Sunil Saxena

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Spin Labels ◽

Electron Resonance ◽

Double Electron ◽

Force Field Parameters ◽

Dynamics Simulations ◽

Double Electron Electron Resonance

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Comparison of Carbohydrate Force Fields Using Gaussian Accelerated Molecular Dynamics Simulations and Development of Force Field Parameters for Heparin-Analogue Pentasaccharides

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.9b00666 ◽

2019 ◽

Vol 59 (11) ◽

pp. 4855-4867 ◽

Cited By ~ 4

Author(s):

Gábor Balogh ◽

Tamás Gyöngyösi ◽

István Timári ◽

Mihály Herczeg ◽

Anikó Borbás ◽

...

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Force Fields ◽

Accelerated Molecular Dynamics ◽

Force Field Parameters ◽

Dynamics Simulations

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Paramfit: Automated optimization of force field parameters for molecular dynamics simulations

Journal of Computational Chemistry ◽

10.1002/jcc.23775 ◽

2014 ◽

Vol 36 (2) ◽

pp. 79-87 ◽

Cited By ~ 53

Author(s):

Robin M. Betz ◽

Ross C. Walker

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Force Field Parameters ◽

Dynamics Simulations ◽

Automated Optimization

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Validation of nitroxyl spin-label force-field parameters through molecular dynamics simulations

Journal of Computational Chemistry ◽

10.1002/jcc.1071 ◽

2001 ◽

Vol 22 (10) ◽

pp. 1113-1123 ◽

Cited By ~ 1

Author(s):

Christopher J. Van Zele ◽

Mark A. Cunningham ◽

Marvin W. Makinen

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Spin Label ◽

Force Field Parameters ◽

Dynamics Simulations

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3P107 Molecular dynamics simulations of β2AR : the comparison of different protein-lipid force field parameters(03. Membrane proteins,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s266_5 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S266

Author(s):

Md. Iqbal Mahmood ◽

Nozomu Kamiya ◽

Hideaki Fujitani ◽

Yamashita Takefumi

Keyword(s):

Molecular Dynamics ◽

Membrane Proteins ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Biophysical Society ◽

Force Field Parameters ◽

Dynamics Simulations

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Force field parameters for S -nitrosocysteine and molecular dynamics simulations of S -nitrosated thioredoxin

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2008.10.017 ◽

2008 ◽

Vol 377 (2) ◽

pp. 612-616 ◽

Cited By ~ 20

Author(s):

Sanghwa Han

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Force Field Parameters ◽

Dynamics Simulations

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Ab initio derived force-field parameters for molecular dynamics simulations of deprotonated amorphous-SiO2 /water interfaces

physica status solidi (b) ◽

10.1002/pssb.201100786 ◽

2011 ◽

Vol 249 (2) ◽

pp. 292-305 ◽

Cited By ~ 52

Author(s):

Anke Butenuth ◽

Gianpietro Moras ◽

Julian Schneider ◽

Mohammad Koleini ◽

Susan Köppen ◽

...

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Amorphous Sio2 ◽

Force Field Parameters ◽

Dynamics Simulations

Download Full-text