Yasuteru Shigeta

38 papers Journal 38
YearRankTypeTitle / Venue / Authors
2026 J jnl
DFDD: A Cloud-Ready Tool for Distance-Guided Fully Dynamic Docking in Host-Guest Complexation.
J. Chem. Inf. Model.
Kowit Hengphasatporn, Lian Duan, Ryuhei Harada, Yasuteru Shigeta
2025 J jnl
Construction of PROTAC-Mediated Ternary Complex Structure Distribution Profiles Using Extensive Conformational Search.
J. Chem. Inf. Model.
Genki Kudo, Takumi Hirao, Ryuhei Harada, Yasuteru Shigeta, Takatsugu Hirokawa, Ryunosuke Yoshino
2025 J jnl
Exploring mimosamycin as a Janus kinase 2 inhibitor: A combined computational and experimental investigation.
Comput. Biol. Chem.
Kamonpan Sanachai, Kowit Hengphasatporn, Supakarn Chamni, Khanit Suwanborirux, Panupong Mahalapbutr, Yasuteru Shigeta, Supaporn Seetaha, Kiattawee Choowongkomon, Thanyada Rungrotmongkol
2025 J jnl
PaCS-Q: Python Toolkits for Path Sampling in MD and QM/MM MD Simulation.
J. Chem. Inf. Model.
Lian Duan, Kowit Hengphasatporn, Yasuteru Shigeta
2024 J jnl
A machine learning potential construction based on radial distribution function sampling.
J. Comput. Chem.
Natsuki Watanabe, Yuta Hori, Hiroki Sugisawa, Tomonori Ida, Mitsuo Shoji, Yasuteru Shigeta
2024 J jnl
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation.
J. Chem. Inf. Model.
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
2024 J jnl
Evaluating solubility, stability, and inclusion complexation of oxyresveratrol with various β-cyclodextrin derivatives using advanced computational techniques and experimental validation.
Comput. Biol. Chem.
Saba Ali, Aamir Aman, Kowit Hengphasatporn, Lipika Oopkaew, Bunyaporn Todee, Ryo Fujiki, Ryuhei Harada, Yasuteru Shigeta, Kuakarun Krusong, Kiattawee Choowongkomon, Warinthorn Chavasiri, Peter Wolschann, Panupong Mahalapbutr, Thanyada Rungrotmongkol
2024 J jnl
Machine learning-guided design of potent darunavir analogs targeting HIV-1 proteases: A computational approach for antiretroviral drug discovery.
J. Comput. Chem.
Hathaichanok Chuntakaruk, Kajjana Boonpalit, Jiramet Kinchagawat, Fahsai Nakarin, Tanatorn Khotavivattana, Chanat Aonbangkhen, Yasuteru Shigeta, Kowit Hengphasatporn, Sarana Nutanong, Thanyada Rungrotmongkol, Supot Hannongbua
2024 J jnl
Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding.
J. Chem. Inf. Model.
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
2024 J jnl
Site Identification and Next Choice Protocol for Hit-to-Lead Optimization.
J. Chem. Inf. Model.
Genki Kudo, Takumi Hirao, Ryunosuke Yoshino, Yasuteru Shigeta, Takatsugu Hirokawa
2023 J jnl
Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score.
J. Comput. Aided Mol. Des.
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
2023 J jnl
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods.
J. Chem. Inf. Model.
Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta
2023 J jnl
Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CL
J. Chem. Inf. Model.
Piyatida Pojtanadithee, Kowit Hengphasatporn, Aphinya Suroengrit, Siwaporn Boonyasuppayakorn, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, I. Putu Sukanadi, Warinthorn Chavasiri, Peter Wolschann, Thierry Langer, Yasuteru Shigeta, Phornphimon Maitarad, Kamonpan Sanachai, Thanyada Rungrotmongkol
2023 J jnl
Pocket to concavity: a tool for the refinement of protein-ligand binding site shape from alpha spheres.
Bioinform.
Genki Kudo, Takumi Hirao, Ryunosuke Yoshino, Yasuteru Shigeta, Takatsugu Hirokawa
2022 J jnl
Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease.
J. Chem. Inf. Model.
Kowit Hengphasatporn, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Warinthorn Chavasiri, Peerapat Visitchanakun, Asada Leelahavanichkul, Wattamon Paunrat, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol, Supot Hannongbua, Yasuteru Shigeta
2022 J jnl
Next generation quantum theory of atoms in molecules for the design of emitters exhibiting thermally activated delayed fluorescence with laser irradiation.
J. Comput. Chem.
Zi Li, Yong Yang, Tianlv Xu, Herbert Früchtl, Tanja Van Mourik, Martin J. Paterson, Yasuteru Shigeta, Steven R. Kirk, Samantha Jenkins
2022 J jnl
Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace.
J. Chem. Inf. Model.
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
2022 J jnl
Structural Validation by the
J. Chem. Inf. Model.
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
2020 J jnl
Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics.
J. Chem. Inf. Model.
Takunori Yasuda, Yasuteru Shigeta, Ryuhei Harada
2020 J jnl
Protein Dynamics and the Folding Degree.
J. Chem. Inf. Model.
Vladimír Sládek, Ryuhei Harada, Yasuteru Shigeta
2019 J jnl
Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations.
J. Chem. Inf. Model.
Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimír Sládek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, Yasuteru Shigeta
2019 J jnl
Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins.
J. Chem. Inf. Model.
Ryuhei Harada, Vladimír Sládek, Yasuteru Shigeta
2019 J jnl
Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency.
J. Chem. Inf. Model.
Ryuhei Harada, Yasuteru Shigeta
2019 J jnl
Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins.
J. Comput. Chem.
Ryuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru Shigeta
2018 J jnl
Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation.
J. Chem. Inf. Model.
Ryuhei Harada, Yasuteru Shigeta
2017 J jnl
Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding.
J. Comput. Chem.
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
2017 J jnl
Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches.
J. Chem. Inf. Model.
Ryuhei Harada, Yasuteru Shigeta
2017 J jnl
Structural dissimilarity sampling with dynamically self-guiding selection.
J. Comput. Chem.
Ryuhei Harada, Yasuteru Shigeta
2017 J jnl
Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins.
J. Comput. Chem.
Ryuhei Harada, Yasuteru Shigeta
2016 J jnl
Refractive indices of organo-metallic and -metalloid compounds: A long-range corrected DFT study.
J. Comput. Chem.
Shintaro Maekawa, Krzysztof Moorthi, Yasuteru Shigeta
2016 J jnl
Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution.
J. Comput. Chem.
Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta
2015 J jnl
Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin.
J. Comput. Chem.
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
2015 J jnl
Protein folding pathways extracted by OFLOOD: Outlier FLOODing method.
J. Comput. Chem.
Ryuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru Shigeta
2014 J jnl
On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase.
J. Comput. Chem.
Takeshi Baba, Ryuhei Harada, Masayoshi Nakano, Yasuteru Shigeta
2013 J jnl
Consistent scheme for computing standard hydrogen electrode and redox potentials.
J. Comput. Chem.
Toru Matsui, Yasutaka Kitagawa, Mitsutaka Okumura, Yasuteru Shigeta, Shigeyoshi Sakaki
2013 J jnl
Finite-field method with unbiased polarizable continuum model for evaluation of the second hyperpolarizability of an open-shell singlet molecule in solvents.
J. Comput. Chem.
Tomoya Inui, Yasuteru Shigeta, Katsuki Okuno, Takeshi Baba, Ryohei Kishi, Masayoshi Nakano
2011 J jnl
An Atomistic Study on Hydrogenation Effects toward Quality Improvement of Program/Erase Cycle of MONOS-Type Memory.
IEICE Trans. Electron.
Akira Otake, Keita Yamaguchi, Katsumasa Kamiya, Yasuteru Shigeta, Kenji Shiraishi
2011 J jnl
Study on Collective Electron Motion in Si-Nano Dot Floating Gate MOS Capacitor.
IEICE Trans. Electron.
Masakazu Muraguchi, Yoko Sakurai, Yukihiro Takada, Shintaro Nomura, Kenji Shiraishi, Mitsuhisa Ikeda, Katsunori Makihara, Seiichi Miyazaki, Yasuteru Shigeta, Tetsuo Endoh