Change in binding states between catabolite activating protein and DNA induced by ligand-binding: molecular dynamics and ab initio fragment molecular orbital calculations

Ryo Anan; Toshiya Nakamura; Kanako Shimamura; Yuki Matsushita; Tatsuya Ohyama; Noriyuki Kurita

doi:10.1007/s00894-019-4087-3

Change in binding states between catabolite activating protein and DNA induced by ligand-binding: molecular dynamics and ab initio fragment molecular orbital calculations

Journal of Molecular Modeling ◽

10.1007/s00894-019-4087-3 ◽

2019 ◽

Vol 25 (7) ◽

Cited By ~ 2

Author(s):

Ryo Anan ◽

Toshiya Nakamura ◽

Kanako Shimamura ◽

Yuki Matsushita ◽

Tatsuya Ohyama ◽

...

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Ab Initio ◽

Molecular Orbital ◽

Molecular Orbital Calculations ◽

Fragment Molecular Orbital

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Proposal of novel natural inhibitors of severe acute respiratory syndrome coronavirus 2 main protease: Molecular docking and ab initio fragment molecular orbital calculations

Biophysical Chemistry ◽

10.1016/j.bpc.2021.106608 ◽

2021 ◽

Vol 275 ◽

pp. 106608

Author(s):

Divya Shaji ◽

Shohei Yamamoto ◽

Ryosuke Saito ◽

Ryo Suzuki ◽

Shunya Nakamura ◽

...

Keyword(s):

Molecular Docking ◽

Severe Acute Respiratory Syndrome ◽

Ab Initio ◽

Molecular Orbital ◽

Molecular Orbital Calculations ◽

Fragment Molecular Orbital ◽

Main Protease ◽

Natural Inhibitors

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Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b09326 ◽

2018 ◽

Vol 123 (5) ◽

pp. 957-973 ◽

Cited By ~ 21

Author(s):

Yoshio Okiyama ◽

Chiduru Watanabe ◽

Kaori Fukuzawa ◽

Yuji Mochizuki ◽

Tatsuya Nakano ◽

...

Keyword(s):

Boltzmann Equation ◽

Ligand Binding ◽

Molecular Orbital ◽

Implicit Solvent ◽

Molecular Orbital Calculations ◽

Binding System ◽

Fragment Molecular Orbital ◽

Poisson Boltzmann ◽

Poisson Boltzmann Equation

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Specific interactions between amyloid-β peptides in an amyloid-β hexamer with three-fold symmetry: Ab initio fragment molecular orbital calculations in water

Chemical Physics Letters ◽

10.1016/j.cplett.2017.01.041 ◽

2017 ◽

Vol 672 ◽

pp. 13-20 ◽

Cited By ~ 6

Author(s):

Hiromi Ishimura ◽

Shogo Tomioka ◽

Ryushi Kadoya ◽

Kanako Shimamura ◽

Akisumi Okamoto ◽

...

Keyword(s):

Ab Initio ◽

Molecular Orbital ◽

Amyloid Β ◽

Molecular Orbital Calculations ◽

Specific Interactions ◽

Fragment Molecular Orbital

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Specific interactions between 2-trans enoyl-acyl carrier protein reductase and its ligand: Protein-ligand docking and ab initio fragment molecular orbital calculations

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2019.02.011 ◽

2019 ◽

Vol 88 ◽

pp. 299-308

Author(s):

Naruedon Phusi ◽

Riku Sato ◽

Takuya Ezawa ◽

Shogo Tomioka ◽

Chayanin Hanwarinroj ◽

...

Keyword(s):

Ab Initio ◽

Molecular Orbital ◽

Acyl Carrier Protein ◽

Ligand Docking ◽

Molecular Orbital Calculations ◽

Carrier Protein ◽

Specific Interactions ◽

Fragment Molecular Orbital

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Molecular dynamics and ab initio molecular orbital calculations on conformational change of amyloid-ß monomers in an in vivo amyloid-ß nonamer

2017 International Conference on Advanced Informatics, Concepts, Theory, and Applications (ICAICTA) ◽

10.1109/icaicta.2017.8090992 ◽

2017 ◽

Author(s):

Shogo Tomioka ◽

Haruki Sougawa ◽

Hiromi Ishimura ◽

Akisumi Okamoto ◽

Noriyuki Kurita ◽

...

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Conformational Change ◽

Molecular Orbital ◽

Molecular Orbital Calculations

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Three-Body Expansion and Generalized Dynamic Fragmentation Improve the Fragment Molecular Orbital-Based Molecular Dynamics (fMO-MD), An ab Initio MD Method

Biophysical Journal ◽

10.1016/j.bpj.2009.12.3113 ◽

2010 ◽

Vol 98 (3) ◽

pp. 573a

Author(s):

Yuto Komeiji ◽

Yuji Mochizuki ◽

Tatsuya Nakano

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Orbital ◽

Fragment Molecular Orbital ◽

Dynamic Fragmentation ◽

Ab Initio Md ◽

Three Body

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2P029 Ab initio fragment molecular orbital calculations on specific interactions between butylcholinesterase and its inhibitors(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s199_5 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S199

Author(s):

Takeru Murakawa ◽

Tomoya Suzuki ◽

Tareq Khan ◽

Noriyuki Kurita

Keyword(s):

Protein Structure ◽

Structure Function ◽

Ab Initio ◽

Annual Meeting ◽

Molecular Orbital ◽

Molecular Orbital Calculations ◽

Specific Interactions ◽

Fragment Molecular Orbital ◽

Biophysical Society

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Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD)

Computational and Theoretical Chemistry ◽

10.1016/j.comptc.2012.02.008 ◽

2012 ◽

Vol 986 ◽

pp. 30-34 ◽

Cited By ~ 18

Author(s):

Hirotoshi Mori ◽

Natsumi Hirayama ◽

Yuto Komeiji ◽

Yuji Mochizuki

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Orbital ◽

Fragment Molecular Orbital ◽

Cis And Trans

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Molecular dynamics simulation of supercritical carbon dioxide fluid with the model potential from ab initio molecular orbital calculations

Chemical Physics Letters ◽

10.1016/0009-2614(96)00397-1 ◽

1996 ◽

Vol 255 (4-6) ◽

pp. 347-349 ◽

Cited By ~ 24

Author(s):

Seiji Tsuzuki ◽

Tadafumi Uchimaru ◽

Masuhiro Mikami ◽

Kazutoshi Tanabe ◽

Takeshi Sako ◽

...

Keyword(s):

Carbon Dioxide ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Supercritical Carbon Dioxide ◽

Ab Initio ◽

Molecular Orbital ◽

Model Potential ◽

Dynamics Simulation ◽

Molecular Orbital Calculations ◽

Supercritical Carbon

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Design of galardine analogs as putative psudolysin inhibitors based on ab initio fragment molecular orbital calculations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1656672 ◽

2019 ◽

Vol 38 (11) ◽

pp. 3307-3317

Author(s):

Takuya Ezawa ◽

Satoshi Sugiyama ◽

Ayami Ara ◽

Ingebrigt Sylte ◽

Noriyuki Kurita

Keyword(s):

Ab Initio ◽

Molecular Orbital ◽

Molecular Orbital Calculations ◽

Fragment Molecular Orbital

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