Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

PLoS ONE ◽

10.1371/journal.pone.0060602 ◽

2013 ◽

Vol 8 (4) ◽

pp. e60602 ◽

Author(s):

Casper Steinmann ◽

Dmitri G. Fedorov ◽

Jan H. Jensen

Keyword(s):

Ab Initio ◽

Molecular Orbital ◽

Enzymatic Catalysis ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital

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Molecular Interactions between Estrogen Receptor and Its Ligand Studied by the ab Initio Fragment Molecular Orbital Method

The Journal of Physical Chemistry B ◽

10.1021/jp065705n ◽

2006 ◽

Vol 110 (47) ◽

pp. 24276-24276 ◽

Author(s):

Kaori Fukuzawa ◽

Yuji Mochizuki ◽

Shigenori Tanaka ◽

Kazuo Kitaura ◽

Tatsuya Nakano

Keyword(s):

Estrogen Receptor ◽

Ab Initio ◽

Molecular Orbital ◽

Molecular Interactions ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital

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Ab Initio Biomolecular Calculations Using Quantum Monte Carlo Combined with the Fragment Molecular Orbital Method

ACS Symposium Series - Advances in Quantum Monte Carlo ◽

10.1021/bk-2007-0953.ch010 ◽

2006 ◽

pp. 141-146 ◽

Author(s):

Ryo Maezono ◽

Hirofumi Watanabe ◽

Shigenori Tanaka

Keyword(s):

Monte Carlo ◽

Ab Initio ◽

Molecular Orbital ◽

Quantum Monte Carlo ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital

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Ab initio study of molecular interactions in higher plant and Galdieria partita Rubiscos with the fragment molecular orbital method

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2007.07.004 ◽

2007 ◽

Vol 361 (2) ◽

pp. 367-372 ◽

Author(s):

Hirofumi Watanabe ◽

Taira Enomoto ◽

Shigenori Tanaka

Keyword(s):

Ab Initio ◽

Molecular Orbital ◽

Molecular Interactions ◽

Orbital Method ◽

Molecular Orbital Method ◽

Ab Initio Study ◽

Higher Plant ◽

Fragment Molecular Orbital

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2P140 Protein-Inhibitor Binding Enthalpy Calculation with ab initio Fragment Molecular Orbital Method(The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s107_1 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S107

Author(s):

Hiroh Miyagawa ◽

Mayumi Endo

Keyword(s):

Ab Initio ◽

Annual Meeting ◽

Molecular Orbital ◽

Orbital Method ◽

Molecular Orbital Method ◽

Protein Inhibitor ◽

Inhibitor Binding ◽

Fragment Molecular Orbital ◽

Biophysical Society ◽

Binding Enthalpy

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2E1558 Protein specific partial charges by Ab-initio fragment molecular orbital method for more accurate protein simulations(Proteins:Property II,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.52.s47_2 ◽

2012 ◽

Vol 52 (supplement) ◽

pp. S47

Author(s):

Le Chang ◽

Shoji Takada

Keyword(s):

Ab Initio ◽

Annual Meeting ◽

Molecular Orbital ◽

Oral Presentation ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital ◽

Partial Charges ◽

Biophysical Society

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Abstract: Towards Highly Accurate Large-Scale Ab Initio Calculations Using Fragment Molecular Orbital Method in GAMESS

2012 SC Companion: High Performance Computing, Networking Storage and Analysis ◽

10.1109/sc.companion.2012.170 ◽

2012 ◽

Author(s):

Maricris L. Mayes ◽

Graham D. Fletcher ◽

Mark S. Gordon

Keyword(s):

Ab Initio Calculations ◽

Ab Initio ◽

Molecular Orbital ◽

Large Scale ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital

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Molecular Interactions between Estrogen Receptor and Its Ligand Studied by the ab Initio Fragment Molecular Orbital Method

The Journal of Physical Chemistry B ◽

10.1021/jp060770i ◽

2006 ◽

Vol 110 (32) ◽

pp. 16102-16110 ◽

Author(s):

Kaori Fukuzawa ◽

Yuji Mochizuki ◽

Shigenori Tanaka ◽

Kazuo Kitaura ◽

Tatsuya Nakano

Keyword(s):

Estrogen Receptor ◽

Ab Initio ◽

Molecular Orbital ◽

Molecular Interactions ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital

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Ab initio quantum-chemical study on emission spectra of bioluminescent luciferases by fragment molecular orbital method

Chemical Physics Letters ◽

10.1016/j.cplett.2009.02.076 ◽

2009 ◽

Vol 472 (1-3) ◽

pp. 118-123 ◽

Author(s):

Ayumu Tagami ◽

Nobuhiro Ishibashi ◽

Dai-ichiro Kato ◽

Naoki Taguchi ◽

Yuji Mochizuki ◽

...

Keyword(s):

Ab Initio ◽

Molecular Orbital ◽

Quantum Chemical ◽

Quantum Chemical Study ◽

Emission Spectra ◽

Chemical Study ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital

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Specific Interactions of Protein-Protein Interaction between Human Programmed Death 1 (PD-1) and its Ligand 1 (PD-L1) with AB Initio Fragment Molecular Orbital Method

Biophysical Journal ◽

10.1016/j.bpj.2017.11.2343 ◽

2018 ◽

Vol 114 (3) ◽

pp. 423a

Author(s):

Ho Cheol Lim ◽

Jung Ho Chun ◽

Sung Bo Hwang ◽

Jong Wan Kim ◽

Kyoung Tae No

Keyword(s):

Ab Initio ◽

Molecular Orbital ◽

Protein Interaction ◽

Orbital Method ◽

Specific Interactions ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital ◽

Protein Protein Interaction ◽

Programmed Death ◽

Programmed Death 1

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VISCANA: Visualized Cluster Analysis of Protein−Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening

Journal of Chemical Information and Modeling ◽

10.1021/ci050262q ◽

2006 ◽

Vol 46 (1) ◽

pp. 221-230 ◽

Author(s):

Shinji Amari ◽

Masahiro Aizawa ◽

Junwei Zhang ◽

Kaori Fukuzawa ◽

Yuji Mochizuki ◽

...

Keyword(s):

Cluster Analysis ◽

Ab Initio ◽

Molecular Orbital ◽

Orbital Method ◽

Molecular Orbital Method ◽

Ligand Interaction ◽

Fragment Molecular Orbital ◽

Ligand Screening ◽

Virtual Ligand Screening ◽

Protein Ligand Interaction

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