| 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 | 322 | 2016 |
| Protein crowding affects hydration structure and dynamics R Harada, Y Sugita, M Feig Journal of the American Chemical Society 134 (10), 4842-4849, 2012 | 237 | 2012 |
| 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 | 169 | 2013 |
| 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 | 157 | 2013 |
| 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 | 92 | 2015 |
| 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 | 72 | 2015 |
| 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 | 65 | 2011 |
| 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 | 58 | 2017 |
| 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 | 55 | 2015 |
| 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 | 38 | 2015 |
| 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 | 33 | 2018 |
| 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 | 32 | 2017 |
| Promising SARS-CoV-2 main protease inhibitor ligand-binding modes evaluated using LB-PaCS-MD/FMO K Hengphasatporn, R Harada, P Wilasluck, P Deetanya, ER Sukandar, ... Scientific Reports 12 (1), 17984, 2022 | 31 | 2022 |
| 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 | 30 | 2017 |
| 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 | 30 | 2016 |
| 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 | 28 | 2016 |
| Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins R Harada, Y Takano, Y Shigeta The Journal of Chemical Physics 140 (12), 2014 | 28 | 2014 |
| 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 | 27 | 2014 |
| 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 | 26 | 2016 |
| Automatic detection of hidden dimensions to obtain appropriate reaction coordinates in the Outlier FLOODing (OFLOOD) method R Harada, T Nakamura, Y Shigeta Chemical Physics Letters 639, 269-274, 2015 | 26 | 2015 |
