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 | 188 | 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 | 163 | 2017 |

Minimum free energy path of ligand-induced transition in adenylate kinase Y Matsunaga, H Fujisaki, T Terada, T Furuta, K Moritsugu, A Kidera PLoS computational biology 8 (6), e1002555, 2012 | 107 | 2012 |

How many dimensions are required to approximate the potential energy landscape of a model protein? T Komatsuzaki, K Hoshino, Y Matsunaga, GJ Rylance, RL Johnston, ... The Journal of chemical physics 122 (8), 2005 | 65 | 2005 |

Phase-space reaction network on a multisaddle energy landscape: HCN isomerization CB Li, Y Matsunaga, M Toda, T Komatsuzaki The Journal of chemical physics 123 (18), 2005 | 49 | 2005 |

Linking *time-series* of single-molecule experiments with molecular dynamics simulations by machine learningY Matsunaga, Y Sugita Elife 7, e32668, 2018 | 48 | 2018 |

Topographical complexity of multidimensional energy landscapes GJ Rylance, RL Johnston, Y Matsunaga, CB Li, A Baba, T Komatsuzaki Proceedings of the National Academy of Sciences 103 (49), 18551-18555, 2006 | 43 | 2006 |

Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB Y Matsunaga, T Yamane, T Terada, K Moritsugu, H Fujisaki, S Murakami, ... Elife 7, e31715, 2018 | 38 | 2018 |

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 |

Extended phase-space methods for enhanced sampling in molecular simulations: a review H Fujisaki, K Moritsugu, Y Matsunaga, T Morishita, L Maragliano Frontiers in bioengineering and biotechnology 3, 125, 2015 | 28 | 2015 |

Protein functional motions: basic concepts and computational methodologies S Fuchigami, H Fujisaki, Y Matsunaga, A Kidera Advancing Theory for Kinetics and Dynamics of Complex, Many‐Dimensional …, 2011 | 28 | 2011 |

Anomalous diffusion in folding dynamics of minimalist protein landscape Y Matsunaga, CB Li, T Komatsuzaki Physical review letters 99 (23), 238103, 2007 | 20 | 2007 |

Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure T Niina, Y Matsunaga, S Takada PLOS Computational Biology 17 (7), e1009215, 2021 | 18 | 2021 |

Influence of structural symmetry on protein dynamics Y Matsunaga, R Koike, M Ota, JRH Tame, A Kidera PLoS One 7 (11), e50011, 2012 | 17 | 2012 |

Regularity in chaotic transitions on multibasin landscapes T Komatsuzaki, K Hoshino, Y Matsunaga Geometric Structures of Phase Space in Multidimensional Chaos: Applications …, 2005 | 17 | 2005 |

Multibasin dynamics in off-lattice minimalist protein landscapes Y Matsunaga, KS Kostov, T Komatsuzaki The Journal of Physical Chemistry A 106 (45), 10898-10907, 2002 | 16 | 2002 |

Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca^{2+}-ATPaseC Kobayashi, Y Matsunaga, J Jung, Y Sugita Proceedings of the National Academy of Sciences 118 (40), e2105507118, 2021 | 15 | 2021 |

Use of single-molecule time-series data for refining conformational dynamics in molecular simulations Y Matsunaga, Y Sugita Current opinion in structural biology 61, 153-159, 2020 | 15 | 2020 |

Non-brownian phase space dynamics of molecules, the nature of their vibrational states, and non-RRKM kinetics DM Leitner, Y Matsunaga, CB Li, T Komatsuzaki, A Shojiguchi, M Toda Advances in Chemical Physics 145, 83, 2011 | 15 | 2011 |

Domain motion enhanced (DoME) model for efficient conformational sampling of multidomain proteins C Kobayashi, Y Matsunaga, R Koike, M Ota, Y Sugita The Journal of Physical Chemistry B 119 (46), 14584-14593, 2015 | 14 | 2015 |