Publications

    1. On-the-fly analysis of molecular dynamics simulation trajectories of proteins using the Bayesian inference method
    2. Naoyuki Miyashita, Yasushige Yonezawa, The Journal of Chemical Physics 147 124108-1-124108-8 2017年9月
  1. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms, Takaharu Mori, Naoyuki Miyashita, Wonpil Im, Michael Feig, Yuji Sugita, Biochimica et Biophysica Acta (BBA) - Biomembranes 1858(7) 1635-1651 2016年
  2. REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function, Naoyuki Miyashita, Suyon Re, Yugi Sugita, International Journal of Quantum Chemistry 115(5) 325-332 2015年3月
  3. Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers., P.-C. Li, N. Miyashita, W. Im, S. Ishido, Y. Sugita, Journal of computational chemistry 35(4) 300-308 2014年2月
  4. Energetics of the Presequence-Binding Poses in Mitochondrial Protein Import Through Tom20, Y. Komuro, N. Miyashita, T. Mori, E. Muneyuki, T. Saitoh, D. Kohda, Y. Sugita, Journal of Physical Chemistry B 117(10) 2864-2871 2013年3月
  5. Recent Applications of Replica-Exchange Molecular Dynamics Simulations of Biomolecules, Yuji Sugita, Naoyuki Miyashita, Pai-Chi Li, Takao Yoda, and Yuko Okamoto, Current Physical Chemistry 2(4) 401-412 2012年12月
  6. Conformational flexibility of N-glycans in solution studied by REMD simulations, Suyong Re, Wataru Nishima, Naoyuki Miyashita, Yuji Sugita, Biophys Rev. 4(3) 179-187 2012年8月
  7. Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution, Wataru Nishima, Naoyuki Miyashita, Yoshiki Yamaguchi, Yuji Sugita, Suyong Re, The Journal of Physical Chemistry 116(29) 8504-8512 2012年6月
  8. The inter-transmembrane region of KSHV MIR2 contributes to B7-2 own regulation, M. Kajikawa, P.-C. Li, E. Goto, N. Miyashita, M. Aoki, M. Mito, S. Ishido, Y. Sugita, Journal of Virology 86(9) 5288-5296 2012年5月
  9. Structural diversity and changes in conformational equilibria of biantennary complex-type N-glycans in water revealed by replica-exchange molecular dynamics simulation., Re S, Miyashita N, Yamaguchi Y, Sugita Y, Biophysical journal 101 L44-6 2011年11月
  10. Functionality mapping on internal surfaces of multidrug transporter AcrB based on molecular theory of solvation: implications for drug efflux pathway., Imai T, Miyashita N, Sugita Y, Kovalenko A, Hirata F, Kidera A, The journal of physical chemistry. B 115 8288-8295 2011年6月
  11. The autoimmune TCR-Ob.2F3 can bind to MBP85-99/HLA-DR2 having an unconventional mode as in TCR-Ob.1A12, Z. Kato, J. N.H. Stern, H. K. Nakamura, N. Miyashita, K. Kuwata, N. Kondo, J. L. Strominger, Molecular Immunology 48(1-3) 314-320 2010年11月
  12. レプリカ交換分子動力学法の生体分子への応用, 宮下 尚之, 杉田 有治, 情報処理学会研究報告. [ハイパフォーマンスコンピューティング] 2010(4) 1-6 2010年10月
  13. Replica-exchange Molecular Dynamics Simulations of Amyloid Precursor Protein Dimer in Membrane, Naoyuki Miyashita, Yuji Sugita, Quantum Bio-Informatics III From Quantum Information to Bio-Informatics 361-368 2010年3月
  14. Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase., Miyashita N, Straub JE, Thirumalai D, Journal of the American Chemical Society 131 17843-17852 2009年12月
  15. レプリカ交換分子動力学法によるアミロイド前駆体蛋白質の膜貫通部位の二量体構造予測, 宮下尚之, 杉田有治, BioSupercomputing Newsletter 1 10-10 2009年10月
  16. Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations., Miyashita N, Straub JE, Thirumalai D, Sugita Y, Journal of the American Chemical Society 131 3438-3439 2009年3月
  17. Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16: a molecular dynamics study., Sugita Y, Miyashita N, Yoda T, Ikeguchi M, Toyoshima C, Biochemistry 45 11752-11761 2006年10月
  18. Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+)., Obara K, Miyashita N, Xu C, Toyoshima I, Sugita Y, Inesi G, Toyoshima C, Proceedings of the National Academy of Sciences of the United States of America 102 14489-14496 2005年10月
  19. Protonation of the acidic residues in the transmembrane cation-binding sites of the ca(2+) pump., Sugita Y, Miyashita N, Ikeguchi M, Kidera A, Toyoshima C, Journal of the American Chemical Society 127 6150-6151 2005年5月
  20. Electronic and Lattice Dynamics in The Photoinduced Ionic-to-Neutral Phase Transition in a One-Dimensional Extended Peierls-Hubbard Model, Naoyuki Miyashita, Makoto Kuwabara, and Kenji Yonemitsu, Journal of Physical Society of Japan, 72(9) 2283-2290 2003年9月
  21. Photoinduced dynamics of ionicity near the neutral-ionic phase boundary in a one-dimensional extended Peierls-Hubbard model, Naoyuki Miyashita, Makoto Kuwabara, and Kenji Yonemitsu, Synthetic Metals 135-136(4) 645-646 2003年4月
  22. Photoexcited states and photoinduced dynamics in electronic phases of MMX-chain systems, Kenji Yonemitsu, Naoyuki Miyashita, and Makoto Kuwabara, Synthetic Metals 135-136(4) 521-522 2003年4月
  23. Coherence recovery and photoinduced phase transitions in one-dimensional halogen-bridged binuclear platinum complexes, Kenji Yonemitsu and Naoyuki Miyashita, Physical Review B 68(7) 075113(9) 2003年8月
  24. Variation mechanisms of ground-state and optical-excitation properties in quasi-one-dimensional two-band electron systems, Kenji Yonemitsu, Makoto Kuwabara, and Naoyuki Miyashita, Molecular Crystals and Liquid Crystals 379(1) 467-474 2002年10月
  25. Domain-Wall Dynamics After Photoexcitations Near neutral-Ionic Phase Transitions, Naoyuki Miyashita, Makoto Kuwabara, and Kenji Yonemitsu, Phase Transitions 75(7-8) 887-893 2002年
  26. Influence of short-range interference on ionization threshold law, Naoyuki Miyashita, Shinichi Watanabe, Michio Matsuzawa, and Joseph H. Macek, Physical Review A 61 014901 1999年12月
  27. Quantum diffraction and threshold law for the Temkin-Poet model of electron-hydrogen ionization, Naoyuki Miyashita, Daiji Kato, and Shinichi Watanabe, Physical Review A 59(6) 4385-4389 1998年6月