Study on Collective Electron Motion in Si-Nano Dot Floating Gate MOS Capacitor. - Masakazu Muraguchi; Yoko Sakurai; Yukihiro Takada; Shintaro Nomura; Kenji Shiraishi; Mitsuhisa Ikeda; Katsunori Makihara; Seiichi Miyazaki; Yasuteru Shigeta; Tetsuo Endoh (IEICE Trans. Electron., 2011)

An Atomistic Study on Hydrogenation Effects toward Quality Improvement of Program/Erase Cycle of MONOS-Type Memory. - Akira Otake; Keita Yamaguchi; Katsumasa Kamiya; Yasuteru Shigeta; Kenji Shiraishi (IEICE Trans. Electron., 2011)

Finite-field method with unbiased polarizable continuum model for evaluation of the second hyperpolarizability of an open-shell singlet molecule in solvents. - Tomoya Inui; Yasuteru Shigeta; Katsuki Okuno; Takeshi Baba; Ryohei Kishi; Masayoshi Nakano (J. Comput. Chem., 2013)

Consistent scheme for computing standard hydrogen electrode and redox potentials. - Toru Matsui; Yasutaka Kitagawa; Mitsutaka Okumura; Yasuteru Shigeta; Shigeyoshi Sakaki (J. Comput. Chem., 2013)

On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase. - Takeshi Baba; Ryuhei Harada; Masayoshi Nakano; Yasuteru Shigeta (J. Comput. Chem., 2014)

Protein folding pathways extracted by OFLOOD: Outlier FLOODing method. - Ryuhei Harada; Tomotake Nakamura; Yu Takano; Yasuteru Shigeta (J. Comput. Chem., 2015)

Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin. - Ryuhei Harada; Yu Takano; Yasuteru Shigeta (J. Comput. Chem., 2015)

Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution. - Ryuhei Harada; Tomotake Nakamura; Yasuteru Shigeta (J. Comput. Chem., 2016)

Refractive indices of organo-metallic and -metalloid compounds: A long-range corrected DFT study. - Shintaro Maekawa; Krzysztof Moorthi; Yasuteru Shigeta (J. Comput. Chem., 2016)

Structural dissimilarity sampling with dynamically self-guiding selection. - Ryuhei Harada; Yasuteru Shigeta (J. Comput. Chem., 2017)

Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins. - Ryuhei Harada; Yasuteru Shigeta (J. Comput. Chem., 2017)

Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding. - Ryuhei Harada; Yu Takano; Yasuteru Shigeta (J. Comput. Chem., 2017)

Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches. - Ryuhei Harada; Yasuteru Shigeta (J. Chem. Inf. Model., 2017)

Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation. - Ryuhei Harada; Yasuteru Shigeta (J. Chem. Inf. Model., 2018)

Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins. - Ryuhei Harada; Ryunosuke Yoshino; Hiroaki Nishizawa; Yasuteru Shigeta (J. Comput. Chem., 2019)

Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency. - Ryuhei Harada; Yasuteru Shigeta (J. Chem. Inf. Model., 2019)

Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins. - Ryuhei Harada; Vladimír Sládek; Yasuteru Shigeta (J. Chem. Inf. Model., 2019)

Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations. - Takaki Tokiwa; Shogo Nakano; Yuta Yamamoto; Takeshi Ishikawa; Sohei Ito; Vladimír Sládek; Kaori Fukuzawa; Yuji Mochizuki; Hiroaki Tokiwa; Fuminori Misaizu; Yasuteru Shigeta (J. Chem. Inf. Model., 2019)

Protein Dynamics and the Folding Degree. - Vladimír Sládek; Ryuhei Harada; Yasuteru Shigeta (J. Chem. Inf. Model., 2020)

Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics. - Takunori Yasuda; Yasuteru Shigeta; Ryuhei Harada (J. Chem. Inf. Model., 2020)

Next generation quantum theory of atoms in molecules for the design of emitters exhibiting thermally activated delayed fluorescence with laser irradiation. - Zi Li; Yong Yang; Tianlv Xu; Herbert Früchtl; Tanja Van Mourik; Martin J. Paterson; Yasuteru Shigeta; Steven R. Kirk; Samantha Jenkins (J. Comput. Chem., 2022)

Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease. - Kowit Hengphasatporn; Patcharin Wilasluck; Peerapon Deetanya; Kittikhun Wangkanont; Warinthorn Chavasiri; Peerapat Visitchanakun; Asada Leelahavanichkul; Wattamon Paunrat; Siwaporn Boonyasuppayakorn; Thanyada Rungrotmongkol; Supot Hannongbua; Yasuteru Shigeta (J. Chem. Inf. Model., 2022)

Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins. - Takunori Yasuda; Rikuri Morita; Yasuteru Shigeta; Ryuhei Harada (J. Chem. Inf. Model., 2022)

Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace. - Takunori Yasuda; Rikuri Morita; Yasuteru Shigeta; Ryuhei Harada (J. Chem. Inf. Model., 2022)

Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score. - Rikuri Morita; Yasuteru Shigeta; Ryuhei Harada (J. Comput. Aided Mol. Des., 2023)

Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. - Ryuhei Harada; Rikuri Morita; Yasuteru Shigeta (J. Chem. Inf. Model., 2023)

Pocket to concavity: a tool for the refinement of protein-ligand binding site shape from alpha spheres. - Genki Kudo; Takumi Hirao; Ryunosuke Yoshino; Yasuteru Shigeta; Takatsugu Hirokawa (Bioinform., 2023)

Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CLpro through Structure-Based Virtual Screening and Experimental Approaches. - 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; et al. (J. Chem. Inf. Model., 2023)

Evaluating solubility, stability, and inclusion complexation of oxyresveratrol with various β-cyclodextrin derivatives using advanced computational techniques and experimental validation. - Saba Ali; Aamir Aman; Kowit Hengphasatporn; Lipika Oopkaew; Bunyaporn Todee; Ryo Fujiki; Ryuhei Harada; Yasuteru Shigeta; Kuakarun Krusong; Kiattawee Choowongkomon; Warinthorn Chavasiri; Peter Wolschann; et al. (Comput. Biol. Chem., 2024)

Site Identification and Next Choice Protocol for Hit-to-Lead Optimization. - Genki Kudo; Takumi Hirao; Ryunosuke Yoshino; Yasuteru Shigeta; Takatsugu Hirokawa (J. Chem. Inf. Model., 2024)

Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding. - Takunori Yasuda; Rikuri Morita; Yasuteru Shigeta; Ryuhei Harada (J. Chem. Inf. Model., 2024)

BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation. - Takunori Yasuda; Rikuri Morita; Yasuteru Shigeta; Ryuhei Harada (J. Chem. Inf. Model., 2024)

Machine learning-guided design of potent darunavir analogs targeting HIV-1 proteases: A computational approach for antiretroviral drug discovery. - Hathaichanok Chuntakaruk; Kajjana Boonpalit; Jiramet Kinchagawat; Fahsai Nakarin; Tanatorn Khotavivattana; Chanat Aonbangkhen; Yasuteru Shigeta; Kowit Hengphasatporn; Sarana Nutanong; Thanyada Rungrotmongkol; Supot Hannongbua (J. Comput. Chem., 2024)

A machine learning potential construction based on radial distribution function sampling. - Natsuki Watanabe; Yuta Hori; Hiroki Sugisawa; Tomonori Ida; Mitsuo Shoji; Yasuteru Shigeta (J. Comput. Chem., 2024)

Exploring mimosamycin as a Janus kinase 2 inhibitor: A combined computational and experimental investigation. - Kamonpan Sanachai; Kowit Hengphasatporn; Supakarn Chamni; Khanit Suwanborirux; Panupong Mahalapbutr; Yasuteru Shigeta; Supaporn Seetaha; Kiattawee Choowongkomon; Thanyada Rungrotmongkol (Comput. Biol. Chem., 2025)

PaCS-Q: Python Toolkits for Path Sampling in MD and QM/MM MD Simulation. - Lian Duan; Kowit Hengphasatporn; Yasuteru Shigeta (J. Chem. Inf. Model., 2025)

Construction of PROTAC-Mediated Ternary Complex Structure Distribution Profiles Using Extensive Conformational Search. - Genki Kudo; Takumi Hirao; Ryuhei Harada; Yasuteru Shigeta; Takatsugu Hirokawa; Ryunosuke Yoshino (J. Chem. Inf. Model., 2025)