Research Scientist Shingo Ito


2016 Ph.D. (Science) Nagoya University, Japan
2013 M.A. (Physics) Nagoya University, Japan
2011 B.S. (Physics) Nagoya University, Japan


2024-present Research Scientist, RIKEN R-CCS, Computational Biophysics Research Team, Japan
2019-2023 Postdoctoral Researcher, RIKEN, Theoretical Molecular Science Laboratory, Japan.
2018-2019 Postdoctoral Researcher, Boston University, U.S.
2016-2018 Postdoctoral Researcher, Naogya University, Japan

Professional Affiliations

Biophysical Society of Japan, Protein Science Society of Japan, The Molecular Simulation Society of Japan


  1. Reaction mechanism of enzyme
  2. Development of free energy calculation
  3. Development of molecular dynamics simulation packages


  1. Free-energy landscapes of transmembrane homodimers by bias-exchange adaptively biased molecular dynamics. S. Ito, Y. Sugita* Biophys. Chem., 307, 107190 (2024).
  2. Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding. S. Ito, K. Yagi, and Y. Sugita* J. Chem. Phys., 158, 115101 (2023).
  3. Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation. Y. Matsunaga, M. Kamiya, H. Oshima, J. Jung, S. Ito, and Y. Sugita* Biophys. Rev., 14, 1503-1512 (2022).
  4. Computational analysis on the allostery of tryptophan synthase: Relationship between α/β-ligand binding and distal domain closure. S. Ito, K. Yagi, and Y. Sugita* J. Phys. Chem. B, 126, 3300-3308 (2022).
  5. Encapsulation of aromatic guests in the bisporphyrin cavity of a double-stranded spiroborate helicate: Thermodynamic and kinetic studies and the encapsulation mechanism. N. Ousaka, S. Yamamoto, H. Iida, T. Iwata, S. Ito, R. Souza, Y. Hijikata, S. Irle, and E. Yashima* J. Org. Chem., 86, 10501–10516 (2021).
  6. Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations. K. Yagi, S. Ito, and Y. Sugita* J. Phys. Chem. B, 125, 4701–4713 (2021).
  7. Multi-level free energy simulation with a staged transformation approach. S. Ito, and Q. Cui* J. Chem. Phys., 153, 044115 (2020).
  8. Water-mediated deracemization of a bisporphyrin helicate assisted by diastereoselective encapsulation of chiral guests. N. Ousaka, S. Yamamoto, H. Iida, T. Iwata, S. Ito, Y. Hijikata, S. Irle, and E. Yashima* Nat. Commum., 10, 1457 (2019).
  9. Quantum chemical replica-exchange umbrella sampling molecular dynamics simulations reveal the formation mechanism of iron phthalocyanine from iron and phthalonitrile. S. Ito, Y. Wang, Y. Okamoto*, S. Irle* J. Chem. Phys., 149, 072332 (2018).
  10. Implementation of replica-exchange umbrella sampling in GAMESS. S. Ito, D. G. Fedorov, Y. Okamoto*, S. Irle* Comput. Phys. Commum., 228, 152-162 (2018).
  11. Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package. S. Ito, S. Irle, Y. Okamoto* Comput. Phys. Commum., 204, 1-10 (2016).
  12. QM/MM free energy simulations: recent progress and challenges. X. Lu, D. Fang, S. Ito, Y. Okamoto, V. Ovchinnikov, Q. Cui* Mol. Sim., 42, 1056-1078 (2016).