An insight of early PrP-E200K aggregation by combined molecular dynamics/fragment molecular orbital approaches

Roberto Paciotti; Loriano Storchi; Alessandro Marrone

doi:10.1002/prot.25621

An insight of early PrP-E200K aggregation by combined molecular dynamics/fragment molecular orbital approaches

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25621 ◽

2018 ◽

Vol 87 (1) ◽

pp. 51-61 ◽

Cited By ~ 2

Author(s):

Roberto Paciotti ◽

Loriano Storchi ◽

Alessandro Marrone

Keyword(s):

Molecular Dynamics ◽

Molecular Orbital ◽

Fragment Molecular Orbital

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Ab initioPath Integral Molecular Dynamics Based on Fragment Molecular Orbital Method

Journal of the Physical Society of Japan ◽

10.1143/jpsj.78.104723 ◽

2009 ◽

Vol 78 (10) ◽

pp. 104723 ◽

Cited By ~ 20

Author(s):

Takatoshi Fujita ◽

Hirofumi Watanabe ◽

Shigenori Tanaka

Keyword(s):

Molecular Dynamics ◽

Molecular Orbital ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital

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Solvatochromic Shifts of Uracil and Cytosine Using a Combined Multireference Configuration Interaction/Molecular Dynamics Approach and the Fragment Molecular Orbital Method†

The Journal of Physical Chemistry A ◽

10.1021/jp901601u ◽

2009 ◽

Vol 113 (45) ◽

pp. 12396-12403 ◽

Cited By ~ 47

Author(s):

Kurt A. Kistler ◽

Spiridoula Matsika

Keyword(s):

Molecular Dynamics ◽

Molecular Orbital ◽

Configuration Interaction ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital ◽

Solvatochromic Shifts

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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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Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation

Journal of Computational Chemistry ◽

10.1002/jcc.21025 ◽

2009 ◽

Vol 30 (1) ◽

pp. 40-50 ◽

Cited By ~ 51

Author(s):

Yuto Komeiji ◽

Takeshi Ishikawa ◽

Yuji Mochizuki ◽

Hiroshi Yamataka ◽

Tatsuya Nakano

Keyword(s):

Molecular Dynamics ◽

Molecular Orbital ◽

Chemical Reactions ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital ◽

Explicit Solvation

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Fragment Molecular Orbital Molecular Dynamics with the Fully Analytic Energy Gradient

Journal of Chemical Theory and Computation ◽

10.1021/ct3007869 ◽

2012 ◽

Vol 8 (12) ◽

pp. 5008-5012 ◽

Cited By ~ 42

Author(s):

Kurt R. Brorsen ◽

Noriyuki Minezawa ◽

Feng Xu ◽

Theresa L. Windus ◽

Mark S. Gordon

Keyword(s):

Molecular Dynamics ◽

Molecular Orbital ◽

Fragment Molecular Orbital ◽

Energy Gradient

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Analytic gradient and molecular dynamics simulations using the fragment molecular orbital method combined with effective potentials

Theoretical Chemistry Accounts ◽

10.1007/s00214-012-1136-8 ◽

2012 ◽

Vol 131 (3) ◽

Cited By ~ 22

Author(s):

Takeshi Nagata ◽

Dmitri G. Fedorov ◽

Kazuo Kitaura

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Orbital ◽

Orbital Method ◽

Molecular Orbital Method ◽

Effective Potentials ◽

Fragment Molecular Orbital ◽

Dynamics Simulations

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Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD)

Chemical Physics Letters ◽

10.1016/j.cplett.2009.11.045 ◽

2010 ◽

Vol 484 (4-6) ◽

pp. 380-386 ◽

Cited By ~ 45

Author(s):

Yuto Komeiji ◽

Yuji Mochizuki ◽

Tatsuya Nakano

Keyword(s):

Molecular Dynamics ◽

Molecular Orbital ◽

Fragment Molecular Orbital ◽

Dynamic Fragmentation ◽

Three Body

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Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation

Applied Physics Express ◽

10.35848/1882-0786/abdac6 ◽

2021 ◽

Vol 14 (2) ◽

pp. 027003

Author(s):

Ryo Hatada ◽

Koji Okuwaki ◽

Kazuki Akisawa ◽

Yuji Mochizuki ◽

Yuma Handa ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Molecular Orbital ◽

Molecular Orbital Calculation ◽

Dynamics Simulation ◽

Statistical Interaction ◽

Fragment Molecular Orbital ◽

Main Protease

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Analytic gradient and molecular dynamics simulations using the fragment molecular orbital method combined with effective potentials

Highlights in Theoretical Chemistry - From Quantum Mechanics to Force Fields ◽

10.1007/978-3-642-34450-3_4 ◽

2012 ◽

pp. 35-49

Author(s):

Takeshi Nagata ◽

Dmitri G. Fedorov ◽

Kazuo Kitaura

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Orbital ◽

Orbital Method ◽

Molecular Orbital Method ◽

Effective Potentials ◽

Fragment Molecular Orbital ◽

Dynamics Simulations

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Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems

Journal of Molecular Structure THEOCHEM ◽

10.1016/j.theochem.2008.07.001 ◽

2009 ◽

Vol 898 (1-3) ◽

pp. 2-7 ◽

Cited By ~ 51

Author(s):

Yuto Komeiji ◽

Yuji Mochizuki ◽

Tatsuya Nakano ◽

Dmitri G. Fedorov

Keyword(s):

Molecular Dynamics ◽

Molecular Orbital ◽

Quantum Simulation ◽

Simulation Tool ◽

Molecular Systems ◽

Fragment Molecular Orbital

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