MEXT "Program for Promoting Researches on the Supercomputer Fugaku"
スーパーコンピュータ「富岳」成果創出加速プログラム 標準課題
Development and application of large-scale simulation-based inferences for biomolecules
生体分子シミュレータを基にした大規模推論システムの開発と応用
Embedded Files
A. Mizutani, C. Tan, Y. Sugita, and S. Takada, “Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study” PLOS Computational Biology 19(7): e1011321 (2023) DOI:10.1371/journal.pcbi.1011321.
R. Yamada, and S. Takada, “Postsynaptic protein assembly in three and two dimensions studied by mesoscopic simulations” Biophysical Journal 122, pp.3395-3410 (2023) DOI:10.1016/j.bpj.2023.07.015.
T. Ishizone, Y. Matsunaga, S. Fuchigami, and K. Nakamura, “Representation of Protein Dynamics Disentangled by Time-Structure-Based Prior” Journal of Chemical Theory and Computation published online (2023) DOI:10.1021/acs.jctc.3c01025.
M. Ikei, R. Miyazaki, K. Monden, Y. Naito, A. Takeuchi, Y. S. Takahashi, Y. Tanaka, K. Murata, T. Mori, M. Ichikawa, and T. Tsukazaki, “YeeD is an essential partner for YeeE-mediated thiosulfate uptake in bacteria and regulates thiosulfate ion decomposition” PLOS Biology 22, e3002601 (2024) DOI:10.1371/journal.pbio.3002601.
R. Toyooka, S. Nishimoto, T. Tendo, T. Horiyama, T. Tachi, and Y. Matsunaga, “Explicit description of viral capsid subunit shapes by unfolding dihedrons” Communications Biology 7, 1509 (2024) DOI:10.1038/s42003-024-07218-x.
Y. Kanaoka, T. Mori, W. Nagaike, S. Itaya, Y. Nonaka, H. Kohga, T. Haruyama, Y. Sugano, R. Miyazaki, M. Ichikawa, T. Uchihashi, and T. Tsukazaki, “AFM observation of protein translocation mediated by one unit of SecYEG-SecA complex” Nature Communications 16, 225 (2025) DOI:10.1038/s41467-024-54875-x.
D. Matsuoka, Y. Sugita, and T. Mori, “An Empirical Biasing Force Constant to Minimize Overfitting in Cryo-EM Flexible Fitting Refinement” Journal of Chemical Information and Modeling 65, 9790-9799 (2025) DOI:10.1021/acs.jcim.5c01424.
H. Kohga, N. Lertpreedakorn, R. Miyazaki, S. Wu, K. Hosoda, H. Tanaka, Y. S. Takahashi, K. Yoshikaie, Y. Kuruma, H. Shigematsu, T. Mori, and T. Tsukazaki, “Phage lysis protein LysM acts as a wedge to block MurJ conformational changes” Science Advances 11, eady8083 (2025) DOI:10.1126/sciadv.ady8083.
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