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ORCIDYasuteru Shigeta
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2020 – today
- 2024
[j32]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:
Evaluating solubility, stability, and inclusion complexation of oxyresveratrol with various β-cyclodextrin derivatives using advanced computational techniques and experimental validation. Comput. Biol. Chem. 112: 108111 (2024)- [j31]Hathaichanok Chuntakaruk, Kajjana Boonpalit, Jiramet Kinchagawat, Fahsai Nakarin, Tanatorn Khotavivattana, Chanat Aonbangkhen, Yasuteru Shigeta, Kowit Hengphasatporn, Sarana Nutanong, Thanyada Rungrotmongkol, Supot Hannongbua:
Machine learning-guided design of potent darunavir analogs targeting HIV-1 proteases: A computational approach for antiretroviral drug discovery. J. Comput. Chem. 45(13): 953-968 (2024) - [j30]Genki Kudo, Takumi Hirao, Ryunosuke Yoshino, Yasuteru Shigeta, Takatsugu Hirokawa:
Site Identification and Next Choice Protocol for Hit-to-Lead Optimization. J. Chem. Inf. Model. 64(11): 4475-4484 (2024) - [j29]Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada:
Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding. J. Chem. Inf. Model. 64(16): 6610-6622 (2024) - 2023
- [j28]Genki Kudo, Takumi Hirao, Ryunosuke Yoshino, Yasuteru Shigeta, Takatsugu Hirokawa:
Pocket to concavity: a tool for the refinement of protein-ligand binding site shape from alpha spheres. Bioinform. 39(4) (2023) - [j27]Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada:
Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score. J. Comput. Aided Mol. Des. 37(4): 217-225 (2023) - [j26]Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta:
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. J. Chem. Inf. Model. 63(1): 259-269 (2023) - [j25]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:
Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CLpro through Structure-Based Virtual Screening and Experimental Approaches. J. Chem. Inf. Model. 63(16): 5244-5258 (2023) - 2022
- [j24]Zi Li, Yong Yang, Tianlv Xu, Herbert Früchtl, Tanja Van Mourik, Martin J. Paterson, Yasuteru Shigeta, Steven R. Kirk, Samantha Jenkins:
Next generation quantum theory of atoms in molecules for the design of emitters exhibiting thermally activated delayed fluorescence with laser irradiation. J. Comput. Chem. 43(3): 206-214 (2022) - [j23]Kowit Hengphasatporn, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Warinthorn Chavasiri, Peerapat Visitchanakun, Asada Leelahavanichkul, Wattamon Paunrat, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol, Supot Hannongbua, Yasuteru Shigeta:
Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease. J. Chem. Inf. Model. 62(6): 1498-1509 (2022) - [j22]Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada:
Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins. J. Chem. Inf. Model. 62(14): 3442-3452 (2022) - [j21]Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada:
Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace. J. Chem. Inf. Model. 62(23): 6217-6227 (2022) - 2020
- [j20]Vladimír Sládek, Ryuhei Harada, Yasuteru Shigeta:
Protein Dynamics and the Folding Degree. J. Chem. Inf. Model. 60(3): 1559-1567 (2020) - [j19]Takunori Yasuda, Yasuteru Shigeta, Ryuhei Harada:
Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics. J. Chem. Inf. Model. 60(8): 4021-4029 (2020)
2010 – 2019
- 2019
- [j18]Ryuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru Shigeta:
Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins. J. Comput. Chem. 40(15): 1530-1537 (2019) - [j17]Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimír Sládek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, Yasuteru Shigeta:
Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations. J. Chem. Inf. Model. 59(1): 25-30 (2019) - [j16]Ryuhei Harada, Yasuteru Shigeta:
Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency. J. Chem. Inf. Model. 59(9): 3919-3926 (2019) - [j15]Ryuhei Harada, Vladimír Sládek, Yasuteru Shigeta:
Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins. J. Chem. Inf. Model. 59(12): 5198-5206 (2019) - 2018
- [j14]Ryuhei Harada, Yasuteru Shigeta:
Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation. J. Chem. Inf. Model. 58(7): 1397-1405 (2018) - 2017
- [j13]Ryuhei Harada, Yu Takano, Yasuteru Shigeta:
Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding. J. Comput. Chem. 38(11): 790-797 (2017) - [j12]Ryuhei Harada, Yasuteru Shigeta:
Structural dissimilarity sampling with dynamically self-guiding selection. J. Comput. Chem. 38(22): 1921-1929 (2017) - [j11]Ryuhei Harada, Yasuteru Shigeta:
Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins. J. Comput. Chem. 38(31): 2671-2674 (2017) - [j10]Ryuhei Harada, Yasuteru Shigeta:
Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches. J. Chem. Inf. Model. 57(12): 3070-3078 (2017) - 2016
- [j9]Ryuhei Harada, Tomotake Nakamura, Yasuteru Shigeta:
Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution. J. Comput. Chem. 37(8): 724-738 (2016) - [j8]Shintaro Maekawa, Krzysztof Moorthi, Yasuteru Shigeta:
Refractive indices of organo-metallic and -metalloid compounds: A long-range corrected DFT study. J. Comput. Chem. 37(32): 2759-2769 (2016) - 2015
- [j7]Ryuhei Harada, Tomotake Nakamura, Yu Takano, Yasuteru Shigeta:
Protein folding pathways extracted by OFLOOD: Outlier FLOODing method. J. Comput. Chem. 36(2): 97-102 (2015) - [j6]Ryuhei Harada, Yu Takano, Yasuteru Shigeta:
Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin. J. Comput. Chem. 36(10): 763-772 (2015) - 2014
- [j5]Takeshi Baba, Ryuhei Harada, Masayoshi Nakano, Yasuteru Shigeta:
On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase. J. Comput. Chem. 35(16): 1240-1247 (2014) - 2013
- [j4]Toru Matsui, Yasutaka Kitagawa, Mitsutaka Okumura, Yasuteru Shigeta, Shigeyoshi Sakaki:
Consistent scheme for computing standard hydrogen electrode and redox potentials. J. Comput. Chem. 34(1): 21-26 (2013) - [j3]Tomoya Inui, Yasuteru Shigeta, Katsuki Okuno, Takeshi Baba, Ryohei Kishi, Masayoshi Nakano:
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. 34(27): 2345-2352 (2013) - 2011
- [j2]Akira Otake, Keita Yamaguchi, Katsumasa Kamiya, Yasuteru Shigeta, Kenji Shiraishi:
An Atomistic Study on Hydrogenation Effects toward Quality Improvement of Program/Erase Cycle of MONOS-Type Memory. IEICE Trans. Electron. 94-C(5): 693-698 (2011) - [j1]Masakazu Muraguchi, Yoko Sakurai, Yukihiro Takada, Shintaro Nomura, Kenji Shiraishi, Mitsuhisa Ikeda, Katsunori Makihara, Seiichi Miyazaki, Yasuteru Shigeta, Tetsuo Endoh:
Study on Collective Electron Motion in Si-Nano Dot Floating Gate MOS Capacitor. IEICE Trans. Electron. 94-C(5): 730-736 (2011)
Coauthor Index
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