フォロー
Ryo Kanada
Ryo Kanada
RIKEN Center for Computational Science
確認したメール アドレス: riken.jp
タイトル
引用先
引用先
CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work
H Kenzaki, N Koga, N Hori, R Kanada, W Li, K Okazaki, XQ Yao, ...
Journal of Chemical Theory and Computation 7 (6), 1979-1989, 2011
2132011
Modeling structural dynamics of biomolecular complexes by coarse-grained molecular simulations
S Takada, R Kanada, C Tan, T Terakawa, W Li, H Kenzaki
Accounts of chemical research 48 (12), 3026-3035, 2015
1372015
Prediction of ALK mutations mediating ALK-TKIs resistance and drug re-purposing to overcome the resistance
K Okada, M Araki, T Sakashita, B Ma, R Kanada, N Yanagitani, A Horiike, ...
EBioMedicine 41, 105-119, 2019
1132019
Molecular dynamics simulation-guided drug sensitivity prediction for lung cancer with rare EGFR mutations
S Ikemura, H Yasuda, S Matsumoto, M Kamada, J Hamamoto, ...
Proceedings of the National Academy of Sciences 116 (20), 10025-10030, 2019
512019
Theoretical model for motility and processivity of two-headed molecular motors
R Kanada, K Sasaki
Physical Review E 67 (6), 061917, 2003
392003
High-precision atomic charge prediction for protein systems using fragment molecular orbital calculation and machine learning
K Kato, T Masuda, C Watanabe, N Miyagawa, H Mizouchi, S Nagase, ...
Journal of chemical information and modeling 60 (7), 3361-3368, 2020
252020
Nucleosome crowding in chromatin slows the diffusion but can promote target search of proteins
R Kanada, T Terakawa, H Kenzaki, S Takada
Biophysical journal 116 (12), 2285-2295, 2019
192019
Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy
K Takaba, C Watanabe, A Tokuhisa, Y Akinaga, B Ma, R Kanada, M Araki, ...
Journal of Computational Chemistry 43 (20), 1362-1371, 2022
182022
Structure-based molecular simulations reveal the enhancement of biased Brownian motions in single-headed kinesin
R Kanada, T Kuwata, H Kenzaki, S Takada
PLoS computational biology 9 (2), e1002907, 2013
182013
Stabilization Mechanism for a Nonfibrillar Amyloid β Oligomer Based on Formation of a Hydrophobic Core Determined by Dissipative Particle Dynamics
R Kawai, S Chiba, K Okuwaki, R Kanada, H Doi, M Ono, Y Mochizuki, ...
ACS chemical neuroscience 11 (3), 385-394, 2020
172020
Thermal ratchets with symmetric potentials
R Kanada, K Sasaki
Journal of the Physical Society of Japan 68 (12), 3759-3762, 1999
161999
Microsecond-timescale MD simulation of EGFR minor mutation predicts the structural flexibility of EGFR kinase core that reflects EGFR inhibitor sensitivity
T Yoshizawa, K Uchibori, M Araki, S Matsumoto, B Ma, R Kanada, Y Seto, ...
NPJ precision oncology 5 (1), 1-11, 2021
102021
Coupling Langevin dynamics with continuum mechanics: exposing the role of sarcomere stretch activation mechanisms to cardiac function
T Washio, S Sugiura, R Kanada, JI Okada, T Hisada
Frontiers in physiology 9, 333, 2018
102018
Exploring Successful Parameter Region for Coarse-Grained Simulation of Biomolecules by Bayesian Optimization and Active Learning
R Kanada, A Tokuhisa, K Tsuda, Y Okuno, K Terayama
Biomolecules 10 (3), 482, 2020
82020
Enhanced Conformational Sampling with an Adaptive Coarse-Grained Elastic Network Model Using Short-Time All-Atom Molecular Dynamics
R Kanada, K Terayama, A Tokuhisa, S Matsumoto, Y Okuno
Journal of chemical theory and computation, 2022
62022
Diffusion enhancement of Brownian motors revealed by a solvable model
R Kanada, R Shinagawa, K Sasaki
Physical Review E 98 (6), 062110, 2018
62018
Efficiency of energy transduction in a molecular chemical engine
K Sasaki, R Kanada, S Amari
Journal of the Physical Society of Japan 76 (2), 023003-023003, 2007
52007
Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns
A Tokuhisa, R Kanada, S Chiba, K Terayama, Y Isaka, B Ma, N Kamiya, ...
Journal of Chemical Information and Modeling 60 (6), 2803-2818, 2020
42020
A thermodynamically consistent monte carlo cross-bridge model with a trapping mechanism reveals the role of stretch activation in heart pumping
K Yoneda, R Kanada, J Okada, M Watanabe, S Sugiura, T Hisada, ...
Frontiers in Physiology, 1622, 2022
32022
Using incomplete Cholesky factorization to increase the time step in molecular dynamics simulations
T Washio, X Cui, R Kanada, J Okada, S Sugiura, Y Okuno, S Takada, ...
Journal of Computational and Applied Mathematics 415, 114519, 2022
22022
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