査読付き論文

2021

  • Case Report: Bayesian Statistical Inference of Experimental Parameters via Biomolecular Simulations: Atomic Force Microscopy

    Sotaro Fuchigami(Kyoto University), Toru Niina(Kyoto University), Shoji Takada(Kyoto University)
  • Linker DNA Length is a Key to Tri-nucleosome Folding

    Hiroo Kenzaki(RIKEN), Shoji Takada(Kyoto University)
  • Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA

    Hisashi Ishida(Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology), Hidetoshi Kono(Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology)
  • New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems

    Jaewoon Jung(RIKEN R-CCS, RIKEN CPR), Chigusa Kobayashi, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Yutaka Ishikawa(RIKEN R-CCS), Kento Kasahara(RIKEN BDR), Yuji Sugita(RIKEN R-CCS, RIKEN BDR, RIKEN CPR), Shigeru Ishiduki, Tatsuo Nishiki, Hikaru Inoue(Fujitsu), Michael Feig(Michigan State University)

2020

  • Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step

    Jaewoon Jung(RIKEN R-CCS, RIKEN CPR), Yuji Sugita(RIKEN R-CCS, RIKEN BDR, RIKEN CPR)
  • Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement

    Tetsuro Nagai(Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo), Shuhei Tsurumaki(Department of Materials Chemistry, Graduate School of Engineering, Nagoya University), Ryo Urano(Department of Materials Chemistry, Graduate School of Engineering, Nagoya University), Kazushi Fujimoto(Department of Materials Chemistry, Graduate School of Engineering, Nagoya University), Wataru Shinoda(Department of Materials Chemistry, Graduate School of Engineering, Nagoya University), Susumu Okazaki(Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo)
  • The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA

    Kiyoto Kamagata(Tohoku University), Kana Ouchi(Tohoku University), Cheng Tan(RIKEN), Eriko Mano(Tohoku University), Sridhar Mandali(University of California), Yining Wu(Tohoku University), Shoji Takada(Kyoto University), Satoshi Takahashi(Tohoku University), Reid C Johnson(University of California)
  • Coarse-grained implicit solvent lipid force field with a compatible resolution to the C-alpha protein representation

    Diego Ugarte La Torre(Kyoto University), Shoji Takada(Kyoto University)
  • Particle Filter Method to Integrate High-Speed Atomic Force Microscopy Measurements with Biomolecular Simulations

    Sotaro Fuchigami(Kyoto University), Toru Niina(Kyoto University), Shoji Takada(Kyoto University)
  • CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations

    Seonghoon Kim(Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University), Hiraku Oshima(RIKEN Center for Biosystems Dynamics Research,), Han Zhang(Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University), Nathan R. Kern(Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University), Suyong Re(Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research), Jumin Lee(Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University), Benoit Roux(Department of Biochemistry and Molecular Biology, The University of Chicago), Yuji Sugita(RIKEN Center for Biosystems Dynamics Research, RIKEN Center for Computational Science,RIKEN Cluster for Pioneering Research), Wei Jiang(Leadership Computing Facility, Argonne National Laboratory), Wonpil Im(Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University)
  • Nucleosome allostery in pioneer transcription factor binding

    Cheng Tan(RIKEN), Shoji Takada(Kyoto University)
  • Pivotal Role of Interdigitation in Interleaflet Interactions: Implications from Molecular Dynamics Simulations

    Sangjae Seo(Nagoya University), Michio Murata(Osaka University), Wataru Shinoda(Nagoya University)
  • Exact long-range Coulombic energy calculation for net charged systems neutralized by uniformly distributed background charge using fast multipole method and its application to efficient free energy calculation

    Ryo Urano(Nagoya University), Wataru Shinoda(Nagoya University), Noriyuki Yoshii(Nagoya University), Susumu Okazaki(Nagoya University)
  • Nucleosomes as allosteric scaffolds for genetic regulation

    Shoji Takada(Kyoto University), Giovanni B Brandani(Kyoto University), Cheng Tan(RIKEN)
  • A new lipid force field (FUJI)

    Nozomu Kamiya(Fujitsu Limited Bio-IT R&D Office, Research Center for Advanced Science and Technology), Megumi Kayanuma(Research Center for Computational Design of Advanced Functional Materials), Hideaki Fujitani(Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo), Keiko Shinoda(Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo)
  • Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase F-O motor

    Shintaroh Kubo(Kyoto University), Toru Niina(Kyoto University), Shoji Takada(Kyoto University)
  • Free energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation

    Kazushi Fujimoto(Department of Materials Chemistry, Nagoya University, Nagoya, Japan), Motohiro Fukai(Department of Materials Chemistry, Nagoya University, Nagoya, Japan), Ryo Urano(Department of Materials Chemistry, Nagoya University, Nagoya, Japan), Wataru Shinoda(Department of Materials Chemistry, Nagoya University, Nagoya, Japan), Tetsuya Ishikawa(Department of Radiological and Medical Laboratory Sciences, Nagoya University, Nagoya, Japan), Katsumi Omagari(Department of Virology and Liver Unit, Nagoya City University, Nagoya, Japan), Yasuhito Tanaka(Department of Virology and Liver Unit, Nagoya City University, Nagoya, Japan), Atsushi Nakagawa(Institute for Protein Research, Osaka University, Suita, Japan), Susumu Okazaki(Department of Materials Chemistry, Nagoya University, Nagoya, Japan)

書籍

2020

  • 分子シミュレーションと実験データを統合する機械学習手法

    松永康佑(埼玉大学)