研究概要

主要論文

• 1. J. Jung, K. Yagi, C. Tan, H. Oshima, T. Mori, I.Yu, Y. Matsunaga,C. Kobayashi, S. Ito, D. Ugarte La Torre, Y. Sugita*
  "GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and QM/MM models",
  J. Phys. Chem. B. 128, 6028-6048 (2024).
• 2. *T. Ishizone*, Y. Matsunaga, S. Fuchigami, and K. Nakamura
  "Representation of Protein Dynamics Disentangled by Time-Structure-Based Prior",
  J. Chem. Theory Comput. 20, 436-450 (2023).
• 3. *Y. Matsunaga*, S. Fuchigami, T. Ogane, and S. Takada
  "End-to-End Differentiable Blind Tip Reconstruction for Noisy Atomic Force Microscopy Images",
  Sci. Rep. 13, 129 (2023)
• 4. Y. Matsunaga, M. Kamiya, H. Oshima, J. Jung, S. Ito, and Y. Sugia*
  "Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation*,
  Biophys. Rev. 14, 1503-1512 (2022).
• 5. T. Ogane, D. Noshiro, T. Ando, A. Yamashita, Y. Sugita, and Y. Matsunaga*
  "Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images*,
  PLoS Comput. Biol. 18, e1010384 (23 pages) (2022).
• 6. Y. Matsunaga, and Y. Sugita*
  "Use of single-molecule time-series data for refining conformational dynamics in molecular simulations*,
  Curr. Opin. Struct. Biol. 61, 153-159 (2020).
• 7. Y. Matsunaga, and Y. Sugita*,
  "Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning*,
  eLife 7, e32668 (2018).
• 8. Y. Matsunaga, and Y. Sugita*,
  "Refining Markov State Models for conformational dynamics using ensemble-averaged data and time-series trajectories*,
  J. Chem. Phys. 148, 241731 (2018).

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