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1.
Molecular Mechanism of Amino Acids for Stabilizing Protein Dispersions
Takahiro Fujii; Ryuhei Harada
Langmuir, to be submitted
(2026)
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2.
Aromatic Fluorination Enhances Hydrophobicity and Antimicrobial Activity of Magainin 2
Suzuri Miyoshi; Koryo Obata; Hiroto Murata; Shinsuke Shigeto (+1 著者) Kohei Sato
ACS Applied Materials & Interfaces, under revision
(2026)
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3.
LB-PaCS-MD Guided Simulations Reveal Catch Bond Mechanism in TCR–pMHC Dissociation
Kun Karnchanapandh; Phichayut Songpipa; Chonnikan Hanpaibool; Ryuhei Harada (+2 著者) Thanyada Rungrotmongkol
Journal of Chemical Information Modeling, in press
(2026)
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4.
Diffusion Mechanism of Human Perforin-1 on Lipid Membrane Surfaces
Yuri Kasubuchi; Ryuhei Harada
The Journal of Physical Chemistry B, under review
(2026)
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5.
Precursor Dimer of 3D Domain Swapping During the Folding Process of Cytochrome c
Cheng Xie; Takahiro Sakai; Hongxu Yang; Ryuhei Harada (+6 著者) Shun Hirota
Journal of the American Chemical Society, under review
(2026)
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6.
Striatal Type I Interferon Responses Drive Disease Progression in the Amyotrophic Lateral Sclerosis
Shogo Tanabe; Akiko Uyeda; Keisuke Sekine; Koryo Obata (+12 著者) Rieko Muramatsu
Nature Neuroscience, under review
(2026)
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7.
Computational Insights into the pH-Dependent Behavior of Ipilimumab-CTLA-4: A Switchable Antibody
Wanda Destiarani; Kowit Hengphasatporn; Yasuteru Shigeta; Ryuhei Harada
Physical Chemistry Chemical Physics
28:
12828
(2026)
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8.
Desorption Dynamics of Interstellar Molecule on Amorphous Solid Water Investigated by Machine Learning Potential-based PaCS-MD Simulation
Natsuki Watanabe; Johannes Kӓstner; Yuta Hori; Yasuteru Shigeta (+1 著者) Ryuhei Harada
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9.
Free Energy Calculation Method Based on Enhanced Sampling of Diverse Protein Conformations Predicted by Artificial Intelligence
Toma Aoki; Ryuhei Harada
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10.
Amide-to-Chloroalkene Substitution for Peptide Backbone Modification to Enhance Membrane Permeability
Sayuri Takeo; Mio Takeda; Chihiro Iio; Ai Sakakibara (+9 著者) Tetsuo Narumi
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11.
DFDD: A Cloud-Ready Tool for Distance-Guided Fully Dynamic Host–Guest Complexation
Kowit Hengphasatporn; Lian Duan; Ryuhei Harada; Yasuteru Shigeta
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12.
Phosphorylation on the N-terminal in Hmt1 Enhances Dimerization by Exposing the Binding Surface
Miyabi Endo; Takunori Yasuda; Rikuri Morita; Tomoaki Mizuno (+1 著者) Ryuhei Harada
The Journal of Physical Chemistry B
130:
723
(2026)
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13.
Construction of PROTAC-Mediated Ternary Complex Structure Distribution Profiles Using Extensive Conformational Search
Genki Kudo; Takumi Hirao; Ryuhei Harada; Yasuteru Shigeta (+1 著者) Ryunosuke Yoshino
Journal of Chemical Information and Modeling
65:
6939
(2025)
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14.
Chemical Diversity within Chaperonins Contributes to Stabilizing Substrate Protein Configurations
Takunori Yasuda; Yoshino Okamoto; Yasuteru Shigeta; Ryuhei Harada
The Journal of Physical Chemistry Letter,
16:
6321
(2025)
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15.
Rational Designed and Engineered Antimicrobial Peptides with High Selectivity and Efficiency Against Phytopathogenic Ralstonia Solanecearum
Melvalia Cristin Manik; Kikrusenuo Kiewhuo; Thanyada Rungrotmongkol; Lian Duan (+4 著者) Alisa Vangnai
Science of the Total Environment
976:
179354
(2025)
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16.
In Silico Study on the Intrusion Process of an Inhibitor into AQP7 Channel Toward Efficient Drug Design
Koryo Obata; Yasuteru Shigeta; Ryuhei Harada
Chemistry Letters
54:
upaf063
(2025)
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17.
PaCS-Q: Enhanced Sampling Techniques in QM/MM Molecular Dynamics Simulations
Lian Duan; Kowit Hengphasatporn; Ryuhei Harada; Yasuteru Shigeta
Journal of Chemical Theory and Computation,
21:
4309
(2025)
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18.
Plug-and-Play Toolkit for Ligand-Binding Path Sampling Parallel Cascade Selection Molecular Dynamics Simulation for AMBER and GROMACS
Ryuhei Harada; Kowit Hengphasatporn; Yasuteru Shigeta
(2025)
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19.
Characterization of Delta-7 Alkenone Desaturase in Haptophytes Emiliania Huxleyi Through the Heterologous Expression in Tisochrysis Lutea
Kohei Yoneda; Chinatsu Kobayashi; Hiroya Araie; Rikuri Morita (+4 著者) Iwane Suzuki
Marine Biotechnology
27:
1
(2025)
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20.
Unveiling the Antiviral Inhibitory Activity of Ebselen and Ebsulfur Derivatives on SARS-CoV-2 Using Machine Learning-based QSAR, LB-PaCS-MD, and Experimental Assay
Silpsiri Sinsulpsiri; Yuji Nishii; Qing-Feng Xu-Xu; Masahiro Miura (+12 著者) Thanyada Rungrotmongkol
Scientific Report
15:
6956
(2025)
