| QM/MM free energy simulations: recent progress and challenges X Lu, D Fang, S Ito, Y Okamoto, V Ovchinnikov, Q Cui Molecular simulation 42 (13), 1056-1078, 2016 | 112 | 2016 |
| Exploring the minimum-energy pathways and free-energy profiles of enzymatic reactions with QM/MM calculations K Yagi, S Ito, Y Sugita The Journal of Physical Chemistry B 125 (18), 4701-4713, 2021 | 32 | 2021 |
| 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, E Yashima Nature communications 10 (1), 1457, 2019 | 26 | 2019 |
| Multi-level free energy simulation with a staged transformation approach S Ito, Q Cui The Journal of Chemical Physics 153 (4), 2020 | 18 | 2020 |
| 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, Y Sugita Biophysical Reviews 14 (6), 1503-1512, 2022 | 16 | 2022 |
| Implementation of replica-exchange umbrella sampling in GAMESS S Ito, DG Fedorov, Y Okamoto, S Irle Computer Physics Communications 228, 152-162, 2018 | 13 | 2018 |
| Computational analysis on the allostery of tryptophan synthase: Relationship between α/β-ligand binding and distal domain closure S Ito, K Yagi, Y Sugita The Journal of Physical Chemistry B 126 (17), 3300-3308, 2022 | 9 | 2022 |
| Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package S Ito, S Irle, Y Okamoto Computer Physics Communications 204, 1-10, 2016 | 8 | 2016 |
| 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, ... The Journal of Organic Chemistry 86 (15), 10501-10516, 2021 | 6 | 2021 |
| GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular … J Jung, K Yagi, C Tan, H Oshima, T Mori, I Yu, Y Matsunaga, C Kobayashi, ... The Journal of Physical Chemistry B, 2024 | 4 | 2024 |
| Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding S Ito, K Yagi, Y Sugita The Journal of Chemical Physics 158 (11), 2023 | 3 | 2023 |
| Free-energy landscapes of transmembrane homodimers by bias-exchange adaptively biased molecular dynamics S Ito, Y Sugita Biophysical Chemistry 307, 107190, 2024 | 2 | 2024 |
| 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 The Journal of Chemical Physics 149 (7), 2018 | 2 | 2018 |
