Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion K Matoba, T Kotani, A Tsutsumi, T Tsuji, T Mori, D Noshiro, Y Sugita, ... Nature structural & molecular biology 27 (12), 1185-1193, 2020 | 301 | 2020 |

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 | 292 | 2016 |

Conformational transition of Sec machinery inferred from bacterial SecYE structures T Tsukazaki, H Mori, S Fukai, R Ishitani, T Mori, N Dohmae, A Perederina, ... Nature 455 (7215), 988-991, 2008 | 282 | 2008 |

Structural basis of Sec-independent membrane protein insertion by YidC K Kumazaki, S Chiba, M Takemoto, A Furukawa, K Nishiyama, Y Sugano, ... Nature 509 (7501), 516-520, 2014 | 252 | 2014 |

GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations J Jung, T Mori, C Kobayashi, Y Matsunaga, T Yoda, M Feig, Y Sugita Wiley Interdisciplinary Reviews: Computational Molecular Science 5 (4), 310-323, 2015 | 184 | 2015 |

GENESIS 1.1: A hybrid‐parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms C Kobayashi, J Jung, Y Matsunaga, T Mori, T Ando, K Tamura, M Kamiya, ... Journal of Computational Chemistry 38 (25), 2193-2206, 2017 | 159 | 2017 |

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms T Mori, N Miyashita, W Im, M Feig, Y Sugita Biochimica et Biophysica Acta (BBA)-Biomembranes 1858 (7), 1635-1651, 2016 | 145 | 2016 |

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 | 86 | 2015 |

Crystal structures of SecYEG in lipidic cubic phase elucidate a precise resting and a peptide-bound state Y Tanaka, Y Sugano, M Takemoto, T Mori, A Furukawa, T Kusakizako, ... Cell reports 13 (8), 1561-1568, 2015 | 78 | 2015 |

Surface-tension replica-exchange molecular dynamics method for enhanced sampling of biological membrane systems T Mori, J Jung, Y Sugita Journal of Chemical Theory and Computation 9 (12), 5629-5640, 2013 | 55 | 2013 |

Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein T Mori, J Jung, C Kobayashi, HM Dokainish, S Re, Y Sugita Biophysical journal 120 (6), 1060-1071, 2021 | 53 | 2021 |

Flexible fitting to cryo‐EM density map using ensemble molecular dynamics simulations O Miyashita, C Kobayashi, T Mori, Y Sugita, F Tama Journal of computational chemistry 38 (16), 1447-1461, 2017 | 53 | 2017 |

The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein HM Dokainish, S Re, T Mori, C Kobayashi, J Jung, Y Sugita Elife 11, e75720, 2022 | 46 | 2022 |

Tunnel formation inferred from the I-form structures of the proton-driven protein secretion motor SecDF A Furukawa, K Yoshikaie, T Mori, H Mori, YV Morimoto, Y Sugano, S Iwaki, ... Cell Reports 19 (5), 895-901, 2017 | 45 | 2017 |

Dynamics of nitric oxide controlled by protein complex in bacterial system E Terasaka, K Yamada, PH Wang, K Hosokawa, R Yamagiwa, ... Proceedings of the National Academy of Sciences 114 (37), 9888-9893, 2017 | 42 | 2017 |

Analysis of lipid surface area in protein–membrane systems combining voronoi tessellation and monte carlo integration methods T Mori, F Ogushi, Y Sugita Journal of computational chemistry 33 (3), 286-293, 2012 | 40 | 2012 |

Dimensionality of collective variables for describing conformational changes of a multi-domain protein Y Matsunaga, Y Komuro, C Kobayashi, J Jung, T Mori, Y Sugita The Journal of Physical Chemistry Letters 7 (8), 1446-1451, 2016 | 34 | 2016 |

Midpoint cell method for hybrid (MPI+ OpenMP) parallelization of molecular dynamics simulations J Jung, T Mori, Y Sugita Journal of computational chemistry 35 (14), 1064-1072, 2014 | 29 | 2014 |

Efficient lookup table using a linear function of inverse distance squared J Jung, T Mori, Y Sugita Journal of Computational Chemistry 34 (28), 2412-2420, 2013 | 26 | 2013 |

Optimized hydrogen mass repartitioning scheme combined with accurate temperature/pressure evaluations for thermodynamic and kinetic properties of biological systems J Jung, K Kasahara, C Kobayashi, H Oshima, T Mori, Y Sugita Journal of Chemical Theory and Computation 17 (8), 5312-5321, 2021 | 25 | 2021 |