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Ryuhei Harada
Ryuhei Harada
Verified email at ccs.tsukuba.ac.jp - Homepage
Title
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Cited by
Year
Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
I Yu, T Mori, T Ando, R Harada, J Jung, Y Sugita, M Feig
Elife 5, e19274, 2016
2802016
Protein crowding affects hydration structure and dynamics
R Harada, Y Sugita, M Feig
Journal of the American Chemical Society 134 (10), 4842-4849, 2012
2232012
Reduced native state stability in crowded cellular environment due to protein–protein interactions
R Harada, N Tochio, T Kigawa, Y Sugita, M Feig
Journal of the American Chemical Society 135 (9), 3696-3701, 2013
1612013
Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway
R Harada, A Kitao
The Journal of chemical physics 139 (3), 035103, 2013
1462013
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology
M Feig, R Harada, T Mori, I Yu, K Takahashi, Y Sugita
Journal of Molecular Graphics and Modelling 58, 1-9, 2015
852015
Simple, yet powerful methodologies for conformational sampling of proteins
R Harada, Y Takano, T Baba, Y Shigeta
Physical chemistry chemical physics 17 (9), 6155-6173, 2015
672015
Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method
R Harada, A Kitao
The Journal of Physical Chemistry B 115 (27), 8806-8812, 2011
592011
Nontargeted parallel cascade selection molecular dynamics for enhancing the conformational sampling of proteins
R Harada, A Kitao
Journal of Chemical Theory and Computation 11 (11), 5493-5502, 2015
522015
Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus
J Fujita, R Harada, Y Maeda, Y Saito, E Mizohata, T Inoue, Y Shigeta, ...
Journal of Structural Biology 198 (2), 65-73, 2017
512017
Protein folding pathways extracted by OFLOOD: Outlier FLOODing method
R Harada, T Nakamura, Y Takano, Y Shigeta
Journal of Computational Chemistry 36 (2), 97-102, 2015
352015
Simple, yet efficient conformational sampling methods for reproducing/predicting biologically rare events of proteins
R Harada
Bulletin of the Chemical Society of Japan 91 (9), 1436-1450, 2018
302018
Efficient conformational search based on structural dissimilarity sampling: applications for reproducing structural transitions of proteins
R Harada, Y Shigeta
Journal of Chemical Theory and Computation 13 (3), 1411-1423, 2017
302017
Temperature‐shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins
R Harada, Y Shigeta
Journal of Computational Chemistry 38 (31), 2671-2674, 2017
282017
Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins
R Harada, Y Takano, Y Shigeta
The Journal of Chemical Physics 140 (12), 2014
272014
Sparsity‐weighted outlier FLOOD ing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution
R Harada, T Nakamura, Y Shigeta
Journal of Computational Chemistry 37 (8), 724-738, 2016
262016
On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase
T Baba, R Harada, M Nakano, Y Shigeta
Journal of Computational Chemistry 35 (16), 1240-1247, 2014
262014
Parallel cascade selection molecular dynamics for efficient conformational sampling and free energy calculation of proteins
A Kitao, R Harada, Y Nishihara, DP Tran
AIP Conference Proceedings 1790 (1), 020013, 2016
252016
A fast convergent simulated annealing algorithm for protein-folding: simulated annealing outlier FLOODing (SA-OFLOOD) method
R Harada, T Nakamura, Y Shigeta
Bulletin of the Chemical Society of Japan 89 (11), 1361-1367, 2016
252016
The fast-folding mechanism of Villin headpiece subdomain studied by multiscale distributed computing
R Harada, A Kitao
Journal of Chemical Theory and Computation 8 (1), 290-299, 2012
252012
Enhanced conformational sampling method for proteins based on the T a B oo S e A rch algorithm: Application to the folding of a mini‐protein, chignolin
R Harada, Y Takano, Y Shigeta
Journal of Computational Chemistry 36 (10), 763-772, 2015
232015
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Articles 1–20