| Large-scale membrane permeability prediction of cyclic peptides crossing a lipid bilayer based on enhanced sampling molecular dynamics simulations M Sugita, S Sugiyama, T Fujie, Y Yoshikawa, K Yanagisawa, M Ohue, ... Journal of chemical information and modeling 61 (7), 3681-3695, 2021 | 51 | 2021 |
| Predicting the Binding Mode of 2-Hydroxypropyl-β-cyclodextrin to Cholesterol by Means of the MD Simulation and the 3D-RISM-KH Theory Y Hayashino, M Sugita, H Arima, T Irie, T Kikuchi, F Hirata The Journal of Physical Chemistry B 122 (21), 5716-5725, 2018 | 24 | 2018 |
| Perspective: Structural fluctuation of protein and Anfinsen’s thermodynamic hypothesis F Hirata, M Sugita, M Yoshida, K Akasaka The Journal of Chemical Physics 148 (2), 2018 | 23 | 2018 |
| Predicting the binding free energy of the inclusion process of 2-hydroxypropyl-β-cyclodextrin and small molecules by means of the MM/3D-RISM method M Sugita, F Hirata Journal of Physics: Condensed Matter 28 (38), 384002, 2016 | 18 | 2016 |
| New protocol for predicting the ligand-binding site and mode based on the 3D-RISM/KH theory M Sugita, M Hamano, K Kasahara, T Kikuchi, F Hirata Journal of Chemical Theory and Computation 16 (4), 2864-2876, 2020 | 17 | 2020 |
| Molecular recognition and self-organization in life phenomena studied by a statistical mechanics of molecular liquids, the rism/3d-rism theory M Sugita, I Onishi, M Irisa, N Yoshida, F Hirata Molecules 26 (2), 271, 2021 | 14 | 2021 |
| Differential mode of cholesterol inclusion with 2‐hydroxypropyl‐cyclodextrins increases safety margin in treatment of Niemann‐Pick disease type C Y Yamada, Y Ishitsuka, Y Kondo, S Nakahara, A Nishiyama, T Takeo, ... British Journal of Pharmacology 178 (13), 2727-2746, 2021 | 13 | 2021 |
| A systematic analysis of the binding affinity between the Pim-1 kinase and its inhibitors based on the MM/3D-RISM/KH method T Hasegawa, M Sugita, T Kikuchi, F Hirata Journal of Chemical Information and Modeling 57 (11), 2789-2798, 2017 | 13 | 2017 |
| Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides Y Hosono, S Uchida, M Shinkai, CE Townsend, CN Kelly, MR Naylor, ... Nature Communications 14 (1), 1416, 2023 | 10 | 2023 |
| Lipid composition is critical for accurate membrane permeability prediction of cyclic peptides by molecular dynamics simulations M Sugita, T Fujie, K Yanagisawa, M Ohue, Y Akiyama Journal of Chemical Information and Modeling 62 (18), 4549-4560, 2022 | 10 | 2022 |
| Incorporating into a Cα Go model the effects of geometrical restriction on Cα atoms caused by side chain orientations M Sugita, T Kikuchi Proteins: Structure, Function, and Bioinformatics 81 (8), 1434-1445, 2013 | 10 | 2013 |
| CycPeptMPDB: A comprehensive database of membrane permeability of cyclic peptides J Li, K Yanagisawa, M Sugita, T Fujie, M Ohue, Y Akiyama Journal of Chemical Information and Modeling 63 (7), 2240-2250, 2023 | 7 | 2023 |
| Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures M Matsuoka, M Sugita, T Kikuchi BMC Research Notes 7, 1-13, 2014 | 7 | 2014 |
| Realization of the structural fluctuation of biomolecules in solution: Generalized Langevin Mode Analysis M Sugita, F Hirata Journal of Computational Chemistry 44 (10), 1031-1039, 2023 | 6 | 2023 |
| Analyses of the folding properties of ferredoxin‐like fold proteins by means of a coarse‐grained Gō model: Relationship between the free energy profiles and folding cores M Sugita, T Kikuchi Proteins: Structure, Function, and Bioinformatics 82 (6), 954-965, 2014 | 6 | 2014 |
| Topological and sequence information predict that foldons organize a partially overlapped and hierarchical structure M Sugita, M Matsuoka, T Kikuchi Proteins: Structure, Function, and Bioinformatics 83 (10), 1900-1913, 2015 | 5 | 2015 |
| Computational Screening of a Functional Cyclodextrin Derivative for Suppressing a Side Effect of Doxorubicin M Sugita, I Kuwano, T Higashi, K Motoyama, H Arima, F Hirata The Journal of Physical Chemistry B 125 (9), 2308-2316, 2021 | 3 | 2021 |
| Prediction device, trained model generation device, prediction method, and trained model generation method Y Akiyama, O Masahito, K Yanagisawa, Y Yoshikawa, M Sugita, T Fujie, ... US Patent App. 17/577,507, 2022 | | 2022 |
| 創薬を見据えた 3D-RISM 理論の応用研究 杉田昌岳， 菊地武司， 平田文男 生物物理 57 (6), 299-301, 2017 | | 2017 |
| Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures T Kikuchi, M Sugita, M Matsuoka | | 2014 |
