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Ikuo Fukuda

A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer–DNA Complex
2014 · Kota Kasahara, Ikuo Fukuda, et al. · PLoS ONE · 180
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Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle
2011 · Ikuo Fukuda, Yasushige Yonezawa, et al. · The Journal of Chemical Physics · 126
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Zero-multipole summation method for efficiently estimating electrostatic interactions in molecular system
2013 · Ikuo Fukuda · The Journal of Chemical Physics · 70
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Non-Ewald methods: theory and applications to molecular systems
2012 · Ikuo Fukuda, Haruki Nakamura · Biophysical Reviews · 64
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Application of zero-dipole summation method to molecular dynamics simulations of a membrane protein system
2013 · Narutoshi Kamiya, Ikuo Fukuda, et al. · Chemical Physics Letters · 57
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Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions
2013 · Tadaaki Mashimo, Yoshifumi Fukunishi, et al. · Journal of Chemical Theory and Computation · 53
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Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor
2017 · Gert-Jan Bekker, Narutoshi Kamiya, et al. · Journal of Chemical Theory and Computation · 49
Simple and accurate scheme to compute electrostatic interaction: Zero-dipole summation technique for molecular system and application to bulk water
2012 · Ikuo Fukuda, Narutoshi Kamiya, et al. · The Journal of Chemical Physics · 49
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Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations
2020 · Gert-Jan Bekker, Ikuo Fukuda, et al. · Scientific Reports · 48
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myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme
2016 · Kota Kasahara, Benson Ma, et al. · Biophysics and Physicobiology · 40
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Tsallis dynamics using the Nosé-Hoover approach
2002 · Ikuo Fukuda, Haruki Nakamura · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · 36
Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method
2011 · Yasushige Yonezawa, Ikuo Fukuda, et al. · Journal of Chemical Theory and Computation · 33
Consistent Molecular Dynamics Scheme Applying the Wolf Summation for Calculating Electrostatic Interaction of Particles
2008 · Ikuo Fukuda, Yasushige Yonezawa, et al. · Journal of the Physical Society of Japan · 26
A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system
2016 · Han Wang, Haruki Nakamura, et al. · The Journal of Chemical Physics · 25
Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations
2021 · Gert-Jan Bekker, Ikuo Fukuda, et al. · Scientific Reports · 24
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Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation
2018 · Kota Kasahara, Shun Sakuraba, et al. · The Journal of Physical Chemistry B · 24
Molecular Dynamics Simulations of Double-Stranded DNA in an Explicit Solvent Model with the Zero-Dipole Summation Method
2013 · Takamasa Arakawa, Narutoshi Kamiya, et al. · PLoS ONE · 23
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The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: Analysis of the accuracy and application to liquid systems
2014 · Ikuo Fukuda, Narutoshi Kamiya, et al. · The Journal of Chemical Physics · 22
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Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism
2019 · Junichi Higo, Kota Kasahara, et al. · Protein Engineering Design and Selection · 19
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Construction of an extended invariant for an arbitrary ordinary differential equation with its development in a numerical integration algorithm
2006 · Ikuo Fukuda, Haruki Nakamura · Physical Review E · 18
Molecular Interaction Mechanism of a 14-3‑3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling
2020 · Junichi Higo, Takeshi Kawabata, et al. · Journal of Chemical Information and Modeling · 17
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Efficiency in the Generation of the Boltzmann−Gibbs Distribution by the Tsallis Dynamics Reweighting Method
2004 · Ikuo Fukuda, Haruki Nakamura · The Journal of Physical Chemistry B · 14
GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics
2020 · Junichi Higo, Ayumi Kusaka, et al. · Biophysics and Physicobiology · 13
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Double density dynamics: realizing a joint distribution of a physical system and a parameter system
2015 · Ikuo Fukuda, Kei Moritsugu · Journal of Physics A Mathematical and Theoretical · 13
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Numerical examination of the extended phase‐space volume‐preserving integrator by the Nosé‐Hoover molecular dynamics equations
2008 · Séverine Queyroy, Haruki Nakamura, et al. · Journal of Computational Chemistry · 12
Works count: 68
Citation count: 1,195
H-index: 19
I10-index: 30
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