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Potentiating Antigen-Specific Antibody Production with Peptides Obtained from In Silico Screening for High-Affinity against MHC-II

Molecules (Basel, Switzerland), 2019-08, Vol.24 (16), p.2949

2019

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Cm3+/Eu3+ induced structural, mechanistic and functional implications for calmodulin

Physical chemistry chemical physics : PCCP, 2019-01, Vol.21 (38), p.21213-21222

2019

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Ca2+-ATPase Molecules as a Calcium-Sensitive Membrane-Endoskeleton of Sarcoplasmic Reticulum

International journal of molecular sciences, 2021-03, Vol.22 (5), p.2624

2021

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Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations

RSC advances, 2021-01, Vol.11 (6), p.3272-3279

2021

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

Chemical physics letters, 2010-01, Vol.484 (4), p.380-386

2010

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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, 2009-01, Vol.30 (1), p.40-50

2009

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Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method

Computational and theoretical chemistry, 2015-02, Vol.1054, p.29-37

2015

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Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study

Journal of computational chemistry, 2006-06, Vol.27 (8), p.948-960

2006

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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, 2012-04, Vol.986, p.30-34

2012

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Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method

Journal of molecular graphics & modelling, 2016-09, Vol.69, p.144-153

2016

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Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin

Journal of computational chemistry, 2007-07, Vol.28 (10), p.1750-1762

2007

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Does Amination of Formaldehyde Proceed Through a Zwitterionic Intermediate in Water? Fragment Molecular Orbital Molecular Dynamics Simulations by Using Constraint Dynamics

Chemistry : a European journal, 2010-06, Vol.16 (22), p.6430-6433

2010

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Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems

Physical chemistry chemical physics : PCCP, 2014-06, Vol.16 (22), p.131-1344

2014

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Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy

Computational and theoretical chemistry, 2014-04, Vol.1034, p.7-16

2014

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Molecular dynamics simulations revealed Ca2+‐dependent conformational change of Calmodulin

FEBS letters, 2002-06, Vol.521 (1-3), p.133-139

2002

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Visualization analysis of inter-fragment interaction energies of CRP–cAMP–DNA complex based on the fragment molecular orbital method

Biophysical chemistry, 2007-10, Vol.130 (1), p.1-9

2007

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Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV‑2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations

The journal of physical chemistry. B, 2024-03, Vol.128 (10), p.2249-2265

2024

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Dynamic Cooperativity of Ligand–Residue Interactions Evaluated with the Fragment Molecular Orbital Method

The journal of physical chemistry. B, 2021-06, Vol.125 (24), p.6501-6512

2021

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How Does an SN2 Reaction Take Place in Solution? Full Ab Initio MD Simulations for the Hydrolysis of the Methyl Diazonium Ion

Journal of the American Chemical Society, 2008-02, Vol.130 (8), p.2396-2397

2008

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Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study

Journal of computational chemistry, 2007-10, Vol.28 (13), p.2237-2239

2007

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Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Møller-Plesset perturbation (MP2.5) scheme

Computational and theoretical chemistry, 2017-02, Vol.1101, p.46-54

2017

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Taking Water into Account with the Fragment Molecular Orbital Method

Methods in molecular biology (Clifton, N.J.), 2020-01, Vol.2114, p.105

2020

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Fragment molecular orbital based interaction analyses on complexes between SARS-CoV-2 RBD variants and ACE2

Japanese Journal of Applied Physics, 2021-09, Vol.60 (9), p.90901

2021

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Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand–protein interaction in a pheromone-binding protein

Computational biology and chemistry, 2005-12, Vol.29 (6), p.434-439

2005

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FMO-MD Simulations on the Hydration of Formaldehyde in Water Solution with Constraint Dynamics

Chemistry : a European journal, 2012-07, Vol.18 (31), p.9714-9721

2012

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Potentiating Antigen-Specific Antibody Production with Peptides Obtained from In Silico Screening for High-Affinity against MHC-II

Cm3+/Eu3+ induced structural, mechanistic and functional implications for calmodulin

Ca2+-ATPase Molecules as a Calcium-Sensitive Membrane-Endoskeleton of Sarcoplasmic Reticulum

Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations

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

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

Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study

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

Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method

Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin

Does Amination of Formaldehyde Proceed Through a Zwitterionic Intermediate in Water? Fragment Molecular Orbital Molecular Dynamics Simulations by Using Constraint Dynamics

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems

Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy

Molecular dynamics simulations revealed Ca2+‐dependent conformational change of Calmodulin

Visualization analysis of inter-fragment interaction energies of CRP–cAMP–DNA complex based on the fragment molecular orbital method

Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV‑2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations

Dynamic Cooperativity of Ligand–Residue Interactions Evaluated with the Fragment Molecular Orbital Method

How Does an SN2 Reaction Take Place in Solution? Full Ab Initio MD Simulations for the Hydrolysis of the Methyl Diazonium Ion

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study

Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Møller-Plesset perturbation (MP2.5) scheme

Taking Water into Account with the Fragment Molecular Orbital Method

Fragment molecular orbital based interaction analyses on complexes between SARS-CoV-2 RBD variants and ACE2

Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand–protein interaction in a pheromone-binding protein

FMO-MD Simulations on the Hydration of Formaldehyde in Water Solution with Constraint Dynamics

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