References

ColDock

  1. K Takemura, C Sato, A Kitao, ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation. The Journal of Physical Chemistry B 122 (29), 7191-7200 (2018).

QM/MM RWFE-SCF 法

  1. QM/MM geometry optimization on extensive free-energy surfaces for examination of enzymatic reactions and design of novel functional properties of proteins. Shigehiko Hayashi*, Yoshihiro Uchida, Taisuke Hasegawa, Masahiro Higashi, Takahiro Kosugi, and Motoshi Kamiya. Annu. Rev. Phys. Chem., 68, 135-154 (2017). DOI: 10.1146/annurev-physchem-052516-050827
  2. An Atomistic Model of a Precursor State of Light-Induced Channel Opening of Channelrhodopsin. Cheng Cheng, Motoshi Kamiya, Mizuki Takemoto, Ryuichiro Ishitani, Osamu Nureki, Norio Yoshida, and Shigehiko Hayashi, Biophysical Journal, 115, 1281-1291 (2018). DOI: 10.1016/j.bpj.2018.08.024
  3. Molecular mechanism of wide photoabsorption spectral shifts of color variants of human cellular retinol binding protein II. Cheng Cheng, Motoshi Kamiya, Yoshihiro Uchida, and Shigehiko Hayashi*, Journal of the American Chemical Society, 137, 13362-13370 (2015). DOI: 10.1021/jacs.5b08316
  4. Atomistic design of microbial opsin-based blue-shifted optogenetics tools. Hideaki E. Kato, Motoshi Kamiya, Seiya Sugo, Jumpei Ito, Reiya Taniguchi, Ayaka Orito, Kunio Hirata, Ayumu Inutsuka, Akihiro Yamanaka, Andrés D. Maturana, Ryuichiro Ishitani, Yuki Sudo, Shigehiko Hayashi, and Osamu Nureki, Nature Communications, 6, 7177 (2015). DOI:10.1038/ncomms8177
  5. Crucial role of protein flexibility in formation of a stable reaction transition state in an alpha-amylase catalysis. Takahiro Kosugi and Shigehiko Hayashi*, Journal of the American Chemical Society, 134, 7045-7055 (2012).