Ikuo Fukuda

发表

myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme

Haruki Nakamura, Kota Kasahara, Yutaka Akiyama, 2016, Biophysics and physicobiology.

Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling.

Yoshifumi Fukunishi, Junichi Higo, Narutoshi Kamiya, 2020, Journal of chemical information and modeling.

Performance evaluation of the zero‐multipole summation method in modern molecular dynamics software

Ikuo Fukuda, Shun Sakuraba, 2018, J. Comput. Chem..

mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories

Haruki Nakamura, Kota Kasahara, Neetha Mohan, 2016, Bioinform..

Numerical Integration Techniques Based on a Geometric View and Application to Molecular Dynamics Simulations

Ikuo Fukuda, Séverine Queyroy, I. Fukuda, 2012 .

Non-Ewald methods: theory and applications to molecular systems

Haruki Nakamura, Ikuo Fukuda, I. Fukuda, 2012, Biophysical Reviews.

Optimization Method by Dynamical Algorithm

Ikuo Fukuda, Shigeru Kameda, Shouichi Masuda, 1999 .

Numerical examination of the extended phase‐space volume‐preserving integrator by the Nosé‐Hoover molecular dynamics equations

Haruki Nakamura, Ikuo Fukuda, Séverine Queyroy, 2009, J. Comput. Chem..

Method for optimization problem using a dynamical system

Ikuo Fukuda, 2000 .

Analysis of multiple data sequences with different distributions: defining common principal component axes by ergodic sequence generation and multiple reweighting composition

Ikuo Fukuda, Kei Moritsugu, 2021, IOP SciNotes.

A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer–DNA Complex

Haruki Nakamura, Ikuo Fukuda, Kota Kasahara, 2014, PloS one.

Consistent Molecular Dynamics Scheme Applying the Wolf Summation for Calculating Electrostatic Interaction of Particles(Atomic and molecular physics)

Haruki Nakamura, Yasushige Yonezawa, Ikuo Fukuda, 2008 .

Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor.

Haruki Nakamura, Yasushi Okuno, Mitsugu Araki, 2017, Journal of chemical theory and computation.

Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method.

Haruki Nakamura, Narutoshi Kamiya, Yasushige Yonezawa, 2011, Journal of chemical theory and computation.

Molecular Dynamics Simulations of Double-Stranded DNA in an Explicit Solvent Model with the Zero-Dipole Summation Method

Haruki Nakamura, Narutoshi Kamiya, Ikuo Fukuda, 2013, PloS one.

Simple and accurate scheme to compute electrostatic interaction: zero-dipole summation technique for molecular system and application to bulk water.

Haruki Nakamura, Narutoshi Kamiya, Yasushige Yonezawa, 2012, The Journal of chemical physics.

Effect of microstructure and hardness on the machinability of medium-carbon chrome-molybdenum steel

Kenji Nakamura, Ikuo Fukuda, Tadahisa Akasawa, 2004 .

Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions.

Haruki Nakamura, Yoshifumi Fukunishi, Narutoshi Kamiya, 2013, Journal of chemical theory and computation.

Zero-multipole summation method for efficiently estimating electrostatic interactions in molecular system.

Ikuo Fukuda, I. Fukuda, 2013, The Journal of chemical physics.

The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems.

Haruki Nakamura, Narutoshi Kamiya, Ikuo Fukuda, 2014, The Journal of chemical physics.

Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism

Haruki Nakamura, Mitsuhito Wada, Yoshifumi Fukunishi, 2019, Protein engineering, design & selection : PEDS.

Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle.

Haruki Nakamura, Yasushige Yonezawa, Ikuo Fukuda, 2011, The Journal of chemical physics.

GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics.

Kentaro Mori, Yoshifumi Fukunishi, Junichi Higo, 2020, Biophysics and physicobiology.

Tsallis dynamics using the Nosé-Hoover approach.

Haruki Nakamura, Ikuo Fukuda, Haruki Nakamura, 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.