金田亮 (Ryo Kanada) - マイポータル

基本情報

所属: 国立研究開発法人理化学研究所計算科学研究センター　HPC／AI駆動型医薬プラットフォーム部門上級研究員

J-GLOBAL ID: 201401099260536480
researchmap会員ID: 7000010638

研究分野

ライフサイエンス / 生物物理学 /

論文

Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model.

Ryo Kanada, Atsushi Tokuhisa, Yusuke Nagasaka, Shingo Okuno, Koichiro Amemiya, Shuntaro Chiba, Gert-Jan Bekker, Narutoshi Kamiya, Koichiro Kato, Yasushi Okuno

Journal of chemical theory and computation 20(1) 7-17 2024年1月9日
Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model

Ryo Kanada, Atsushi Tokuhisa, Yusuke Nagasaka, Shingo Okuno, Koichiro Amemiya, Shuntaro Chiba, Gert Jan Bekker, Narutoshi Kamiya, Koichiro Kato, Yasushi Okuno

Journal of Chemical Theory and Computation 2023年
Using incomplete Cholesky factorization to increase the time step in molecular dynamics simulations

Takumi Washio, Xiaoke Cui, Ryo Kanada, Jun-ichi Okada, Seiryo Sugiura, Yasushi Okuno, Shoji Takada, Toshiaki Hisada

Journal of Computational and Applied Mathematics 2022年12月査読有り
Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy

Kenichiro Takaba, Chiduru Watanabe, Atsushi Tokuhisa, Yoshinobu Akinaga, Biao Ma, Ryo Kanada, Mitsugu Araki, Yasushi Okuno, Yusuke Kawashima, Hirotomo Moriwaki …

Journal of Computational Chemistry 43(20) 1362-1371 2022年7月30日
Enhanced Conformational Sampling with an Adaptive Coarse-Grained Elastic Network Model Using Short-Time All-Atom Molecular Dynamics.

Ryo Kanada, Kei Terayama, Atsushi Tokuhisa, Shigeyuki Matsumoto, Yasushi Okuno

Journal of chemical theory and computation 2022年3月24日査読有り筆頭著者責任著者
A thermodynamically consistent monte carlo cross-bridge model with a trapping mechanism reveals the role of stretch activation in heart pumping.

Kazunori Yoneda, Ryo Kanada, Jun-Ichi Okada, Masahiro Watanabe, Seiryo Sugiura, Toshiaki Hisada, Takumi Washio

Frontiers in physiology 13 855303-855303 2022年
Microsecond-timescale MD simulation of EGFR minor mutation predicts the structural flexibility of EGFR kinase core that reflects EGFR inhibitor sensitivity

Takahiro Yoshizawa, Ken Uchibori, Mitsugu Araki, Shigeyuki Matsumoto, Biao Ma, Ryo Kanada, Yosuke Seto, Tomoko Oh-hara, Sumie Koike, Ryo Ariyasu …

npj Precision Oncology 5(1) 2021年12月査読有り
Semi-Implicit Time Integration with Hessian Eigenvalue Corrections for a Larger Time Step in Molecular Dynamics Simulations

Takumi Washio, Ryo Kanada, Xiaoke Cui, Jun Ichi Okada, Seiryo Sugiura, Shoji Takada, Toshiaki Hisada

Journal of Chemical Theory and Computation 2021年査読有り
High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning

Koichiro Kato, Tomohide Masuda, Chiduru Watanabe, Naoki Miyagawa, Hideo Mizouchi, Shumpei Nagase, Kikuko Kamisaka, Kanji Oshima, Satoshi Ono, Hiroshi Ueda …

JOURNAL OF CHEMICAL INFORMATION AND MODELING 60(7) 3361-3368 2020年7月査読有り
Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns

Atsushi Tokuhisa, Ryo Kanada, Shuntaro Chiba, Kei Terayama, Yuta Isaka, Biao Ma, Narutoshi Kamiya, Yasushi Okuno

JOURNAL OF CHEMICAL INFORMATION AND MODELING 60(6) 2803-2818 2020年6月査読有り
Exploring Successful Parameter Region for Coarse-Grained Simulation of Biomolecules by Bayesian Optimization and Active Learning

Ryo Kanada, Atsushi Tokuhisa, Koji Tsuda, Yasushi Okuno, Kei Terayama

Biomolecules 10(3) 482-482 2020年3月21日査読有り筆頭著者責任著者
Stabilization Mechanism for a Nonfibrillar Amyloid β Oligomer Based on Formation of a Hydrophobic Core Determined by Dissipative Particle Dynamics

Ryoko Kawai, Shuntaro Chiba, Koji Okuwaki, Ryo Kanada, Hideo Doi, Masahiro Ono, Yuji Mochizuki, Yasushi Okuno

ACS Chemical Neuroscience 11(3) 385-394 2020年2月5日査読有り
Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins

Ryo Kanada, Tsuyoshi Terakawa, Hiroo Kenzaki, Shoji Takada

BIOPHYSICAL JOURNAL 116(12) 2285-2295 2019年6月査読有り筆頭著者
Molecular dynamics simulation-guided drug sensitivity prediction for lung cancer with rare EGFR mutations.

Shinnosuke Ikemura, Hiroyuki Yasuda, Shingo Matsumoto, Mayumi Kamada, Junko Hamamoto, Keita Masuzawa, Keigo Kobayashi, Tadashi Manabe, Daisuke Arai, Ichiro Nakachi …

Proceedings of the National Academy of Sciences of the United States of America 116(20) 10025-10030 2019年5月14日査読有り
Prediction of ALK mutations mediating ALK-TKIs resistance and drug re-purposing to overcome the resistance

Koutaroh Okada, Mitsugu Araki, Takuya Sakashita, Biao Ma, Ryo Kanada, Noriko Yanagitani, Atsushi Horiike, Sumie Koike, Tomoko Oh-hara, Kana Watanabe …

EBIOMEDICINE 41 105-119 2019年3月査読有り
Diffusion Enhancement of Brownian Motors Revealed by a Solvable Model

Ryo Kanada, Ryota Shinagawa, Kazuo Sasaki

PHYSICAL REVIEW E 98(6) 2018年5月21日査読有り筆頭著者
Coupling Langevin Dynamics With Continuum Mechanics: Exposing the Role of Sarcomere Stretch Activation Mechanisms to Cardiac Function

Takumi Washio, Seiryo Sugiura, Ryo Kanada, Jun-Ichi Okada, Toshiaki Hisada

FRONTIERS IN PHYSIOLOGY 9 333-333 2018年4月査読有り
Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations

Shoji Takada, Ryo Kanada, Cheng Tan, Tsuyoshi Terakawa, Wenfei Li, Hiroo Kenzaki

ACCOUNTS OF CHEMICAL RESEARCH 48(12) 3026-3035 2015年12月査読有り
Nucleotide-dependent structural fluctuations and regulation of microtubule-binding affinity of KIF1A

Ryo Kanada, Fumiko Takagi, Macoto Kikuchi

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 83(5) 809-819 2015年5月査読有り
Energetics of the single-headed kinesin KIF1A

Ryo Kanada, Kazuo Sasaki

PHYSICAL REVIEW E 88(2) 022711-022711 2013年8月査読有り筆頭著者

もっとみる

MISC

Allosterically Regulated Structural Fluctuation and Microtubule-Binding Affinity of KiF1A-A Simulation Study of Coarse-Grained Model -

Macoto Kikuchi, Ryo Kanada, Fumiko Takagi

BIOPHYSICAL JOURNAL 110(3) 459A-459A 2016年2月査読有り
3P028 粗視化分子シミュレーションによるMEK1-ERK2 相互作用の調査(01B. 蛋白質:構造機能相関,ポスター,第52回日本生物物理学会年会(2014年度))

Kanada Ryo, Takada Shoji

生物物理 54(1) S253 2014年
2P047 粗視化シミュレーションによるリン酸化酵素複合体(MEK1-ERK2)のドッキングダイナミクス(01B.蛋白質:構造機能相関,ポスター,日本生物物理学会年会第51回(2013年度))

Kanada Ryo, Takada Shoji

生物物理 53(1) S166 2013年
1PS037 キネシンのヘッド間張力がヌクレオチド結合部位に与える影響 : 分子シミュレーションによる調査(日本生物物理学会第50回年会(2012年度))

Kanada Ryo, Makino Tsukasa, Tomishige Michio, Takada Shoji

生物物理 52 S80 2012年
Structural Basis for the Coordinated Processive Movement of Kinesin-1 studied by Structural and Single Molecule Analyses

Tsukasa Makino, Teppei Mori, Ryo Kanada, Ken-ichi Miyazono, Shoji Takada, Masaru Tanokura, Michio Tomishige

BIOPHYSICAL JOURNAL 100(3) 120-121 2011年2月査読有り
Mechanism of Unidirectional Move of KIF1A Motor Studied by Coarse-Grained Simulations

Ryo Kanada, Takeshi Kuwata, Hiroo Kenzaki, Shoji Takada

BIOPHYSICAL JOURNAL 98(3) 167A-167A 2010年1月査読有り
Biomolecular Coarse-Grained Simulation Program CafeMol

Hiroo Kenzaki, Nobuyasu Koga, Shinji Fujiwara, Naoto Hori, Ryo Kanada, Kei-ichi Okazaki, Xin-Qiu Yao, Wenfei Li, Shoji Takada

BIOPHYSICAL JOURNAL 98(3) 574A-574A 2010年1月査読有り
Molecular Simulation Study of Kinesin: Coupling between ATPase Domain Conformational Change and Mechanical Stepping

Ryo Kanada, Kei-ichi Okazaki, Shoji Takada

BIOPHYSICAL JOURNAL 96(3) 136A-136A 2009年2月査読有り
Structural Fluctuations of Microtubule Binding Site of KIF1A in Different Nucleotide States

Ryo Kanada, Fumiko Takagi, Macoto Kikuchi

2008年1月31日

書籍等出版物

in silico創薬におけるスクリーニングの高速化・高精度化技術

技術情報協会

技術情報協会 2018年1月 (ISBN: 9784861046889)

担当経験のある科目(授業)

所属学協会

共同研究・競争的資金等の研究課題

全原子モデルの併用と機械学習手法の適用による粗視化分子モデルの高精度化

日本学術振興会科学研究費助成事業基盤研究(C) 基盤研究(C) 2019年4月 - 2022年3月

金田亮
分子モーターの理論モデル

日本学術振興会科学研究費助成事業特別研究員奨励費特別研究員奨励費 2000年 - 2002年

金田亮