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ArticlesPeer ReviewedFull Text
Promising SARS-CoV-2 main protease inhibitor ligand-binding modes evaluated using LB-PaCS-MD/FMO
Author / Creator:Hengphasatporn, Kowit ; Harada, Ryuhei ; Wilasluck, Patcharin ; Deetanya, Peerapon ; Sukandar, Edwin R. ; Chavasiri, Warinthorn ; Suroengrit, Aphinya ; Boonyasuppayakorn, Siwaporn ; Rungrotmongkol, Thanyada ; Wangkanont, Kittikhun ; Shigeta, Yasuteru
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2022-10, Vol.12 (1), p.17984-16, Article 17984
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Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score
Author / Creator:Morita, Rikuri ; Shigeta, Yasuteru ; Harada, Ryuhei
Publisher:Cham: Springer International Publishing
Journal title:Journal of computer-aided molecular design, 2023-04, Vol.37 (4), p.217-225
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pyProGA—A PyMOL plugin for protein residue network analysis
Author / Creator:Sladek, Vladimir ; Yamamoto, Yuta ; Harada, Ryuhei ; Shoji, Mitsuo ; Shigeta, Yasuteru ; Sladek, Vladimir
Publisher:San Francisco: Public Library of Science
Journal title:PloS one, 2021-07, Vol.16 (7), p.e0255167-e0255167
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FMO-guided design of darunavir analogs as HIV-1 protease inhibitors
Author / Creator:Chuntakaruk, Hathaichanok ; Hengphasatporn, Kowit ; Shigeta, Yasuteru ; Aonbangkhen, Chanat ; Lee, Vannajan Sanghiran ; Khotavivattana, Tanatorn ; Rungrotmongkol, Thanyada ; Hannongbua, Supot
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2024-02, Vol.14 (1), p.3639-3639, Article 3639
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Identification of novel TMEM16A blockers through integrated virtual screening, molecular dynamics, and experimental studies
Author / Creator:Sangkhawasi, Mattanun ; Pitaktrakul, Wichuda ; Khumjiang, Rungtiwa ; Shigeta, Yasuteru ; Muanprasat, Chatchai ; Hengphasatporn, Kowit ; Rungrotmongkol, Thanyada
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2025-04, Vol.15 (1), p.15065-11, Article 15065
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Autism-associated mutation in Hevin/Sparcl1 induces endoplasmic reticulum stress through structural instability
Author / Creator:Taketomi, Takumi ; Yasuda, Takunori ; Morita, Rikuri ; Kim, Jaehyun ; Shigeta, Yasuteru ; Eroglu, Cagla ; Harada, Ryuhei ; Tsuruta, Fuminori
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2022-07, Vol.12 (1), p.11891-11891, Article 11891
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Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD
Author / Creator:Aida, Hayato ; Shigeta, Yasuteru ; Harada, Ryuhei
Publisher:Switzerland: MDPI AG
Journal title:Materials, 2022-02, Vol.15 (4), p.1490
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Residue Folding Degree—Relationship to Secondary Structure Categories and Use as Collective Variable
Author / Creator:Sladek, Vladimir ; Harada, Ryuhei ; Shigeta, Yasuteru
Publisher:Switzerland: MDPI AG
Journal title:International journal of molecular sciences, 2021-12, Vol.22 (23), p.13042
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Prediction of the binding mechanism of a selective DNA methyltransferase 3A inhibitor by molecular simulation
Author / Creator:Kudo, Genki ; Hirao, Takumi ; Harada, Ryuhei ; Hirokawa, Takatsugu ; Shigeta, Yasuteru ; Yoshino, Ryunosuke
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2024-06, Vol.14 (1), p.13508-9, Article 13508
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Dibromopinocembrin and Dibromopinostrobin Are Potential Anti-Dengue Leads with Mild Animal Toxicity
Author / Creator:Boonyasuppayakorn, Siwaporn ; Saelee, Thanaphon ; Visitchanakun, Peerapat ; Leelahavanichkul, Asada ; Hengphasatporn, Kowit ; Shigeta, Yasuteru ; Huynh, Thao Nguyen Thanh ; Chu, Justin Jang Hann ; Rungrotmongkol, Thanyada ; Chavasiri, Warinthorn
Publisher:Switzerland: MDPI AG
Journal title:Molecules (Basel, Switzerland), 2020-09, Vol.25 (18), p.4154
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ArticlesPeer ReviewedFull Text
Polysulfur-based bulking of dynamin-related protein 1 prevents ischemic sulfide catabolism and heart failure in mice
Author / Creator:Nishimura, Akiyuki ; Ogata, Seiryo ; Tang, Xiaokang ; Hengphasatporn, Kowit ; Umezawa, Keitaro ; Sanbo, Makoto ; Hirabayashi, Masumi ; Kato, Yuri ; Ibuki, Yuko ; Kumagai, Yoshito ; Kobayashi, Kenta ; Kanda, Yasunari ; Urano, Yasuteru ; Shigeta, Yasuteru ; Akaike, Takaaki ; Nishida, Motohiro
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2025-01, Vol.16 (1), p.276-17, Article 276
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ArticlesPeer ReviewedFull Text
Design, synthesis, in vitro, in silico, and SAR studies of flavone analogs towards anti-dengue activity
Author / Creator:Patigo, Apinya ; Hengphasatporn, Kowit ; Cao, Van ; Paunrat, Wattamon ; Vijara, Natthanan ; Chokmahasarn, Thamonwan ; Maitarad, Phornphimon ; Rungrotmongkol, Thanyada ; Shigeta, Yasuteru ; Boonyasuppayakorn, Siwaporn ; Khotavivattana, Tanatorn
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2022-12, Vol.12 (1), p.21646-18, Article 21646
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ArticlesPeer ReviewedFull Text
Structure—yeast α-glucosidase inhibitory activity relationship of 9-O-berberrubine carboxylates
Author / Creator:Nguyen, Duy Vu ; Hengphasatporn, Kowit ; Danova, Ade ; Suroengrit, Aphinya ; Boonyasuppayakorn, Siwaporn ; Fujiki, Ryo ; Shigeta, Yasuteru ; Rungrotmongkol, Thanyada ; Chavasiri, Warinthorn
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2023-11, Vol.13 (1), p.18865-18865, Article 18865
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ArticlesPeer ReviewedFull Text
A Free-Energy Landscape Analysis of Calmodulin Obtained from an NMR Data-Utilized Multi-Scale Divide-and-Conquer Molecular Dynamics Simulation
Author / Creator:Shimoyama, Hiromitsu ; Shigeta, Yasuteru
Publisher:Basel: MDPI AG
Journal title:Life (Basel, Switzerland), 2021-11, Vol.11 (11), p.1241
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Structural and thermodynamic insights into antibody light chain tetramer formation through 3D domain swapping
Author / Creator:Sakai, Takahiro ; Mashima, Tsuyoshi ; Kobayashi, Naoya ; Ogata, Hideaki ; Duan, Lian ; Fujiki, Ryo ; Hengphasatporn, Kowit ; Uda, Taizo ; Shigeta, Yasuteru ; Hifumi, Emi ; Hirota, Shun
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2023-12, Vol.14 (1), p.7807-7807, Article 7807
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ArticlesPeer ReviewedFull Text
Computational Analysis Reveals a Critical Point Mutation in the N-Terminal Region of the Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with Canine Distemper Vir...
Author / Creator:Yamamoto, Yuta ; Nakano, Shogo ; Seki, Fumio ; Shigeta, Yasuteru ; Ito, Sohei ; Tokiwa, Hiroaki ; Takeda, Makoto
Publisher:Switzerland: MDPI AG
Journal title:Molecules (Basel, Switzerland), 2021-02, Vol.26 (5), p.1262
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GPNMB is a novel binding partner of FGFR1 that affects tumorigenic potential through AKT phosphorylation in TNBC
Author / Creator:Elhinnawi, Manar A. ; Okita, Yukari ; Shigematsu, Katsunobu ; Abdelaziz, Mohammed ; Shiratani, Rie ; Kawanishi, Kunio ; Hengphasatporn, Kowit ; Dang Cao, Thuy Linh ; Shigeta, Yasuteru ; Kato, Mitsuyasu
Publisher:England: John Wiley & Sons, Inc
Journal title:Cancer science, 2025-02, Vol.116 (2), p.432-443
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Lichen-Derived Diffractaic Acid Inhibited Dengue Virus Replication in a Cell-Based System
Author / Creator:Loeanurit, Naphat ; Tuong, Truong Lam ; Nguyen, Van-Kieu ; Vibulakhaophan, Vipanee ; Hengphasatporn, Kowit ; Shigeta, Yasuteru ; Ho, Si Xian ; Chu, Justin Jang Hann ; Rungrotmongkol, Thanyada ; Chavasiri, Warinthorn ; Boonyasuppayakorn, Siwaporn
Publisher:Switzerland: MDPI AG
Journal title:Molecules (Basel, Switzerland), 2023-01, Vol.28 (3), p.974
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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
Author / Creator:Sinsulpsiri, Silpsiri ; Nishii, Yuji ; Xu-Xu, Qing-Feng ; Miura, Masahiro ; Wilasluck, Patcharin ; Salamteh, Kanokwan ; Deetanya, Peerapon ; Wangkanont, Kittikhun ; Suroengrit, Aphinya ; Boonyasuppayakorn, Siwaporn ; Duan, Lian ; Harada, Ryuhei ; Hengphasatporn, Kowit ; Shigeta, Yasuteru ; Shi, Liyi ; Maitarad, Phornphimon ; Rungrotmongkol, Thanyada
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2025-02, Vol.15 (1), p.6956-12, Article 6956
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Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography
Author / Creator:Maity, Basudev ; Shoji, Mitsuo ; Luo, Fangjia ; Nakane, Takanori ; Abe, Satoshi ; Owada, Shigeki ; Kang, Jungmin ; Tono, Kensuke ; Tanaka, Rie ; Pham, Thuc Toan ; Kojima, Mariko ; Hishikawa, Yuki ; Tanaka, Junko ; Tian, Jiaxin ; Nagama, Misaki ; Suzuki, Taiga ; Noya, Hiroki ; Nakasuji, Yuto ; Asanuma, Asuka ; Yao, Xinchen ; Iwata, So ; Shigeta, Yasuteru ; Nango, Eriko ; Ueno, Takafumi
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-06, Vol.15 (1), p.5518-12, Article 5518
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Showing 1 to 20 of 43 results

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Promising SARS-CoV-2 main protease inhibitor ligand-binding modes evaluated using LB-PaCS-MD/FMO

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Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score

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pyProGA—A PyMOL plugin for protein residue network analysis

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FMO-guided design of darunavir analogs as HIV-1 protease inhibitors

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Identification of novel TMEM16A blockers through integrated virtual screening, molecular dynamics, and experimental studies

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Autism-associated mutation in Hevin/Sparcl1 induces endoplasmic reticulum stress through structural instability

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Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD

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Residue Folding Degree—Relationship to Secondary Structure Categories and Use as Collective Variable

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Prediction of the binding mechanism of a selective DNA methyltransferase 3A inhibitor by molecular simulation

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Dibromopinocembrin and Dibromopinostrobin Are Potential Anti-Dengue Leads with Mild Animal Toxicity

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Polysulfur-based bulking of dynamin-related protein 1 prevents ischemic sulfide catabolism and heart failure in mice

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Design, synthesis, in vitro, in silico, and SAR studies of flavone analogs towards anti-dengue activity

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Structure—yeast α-glucosidase inhibitory activity relationship of 9-O-berberrubine carboxylates

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A Free-Energy Landscape Analysis of Calmodulin Obtained from an NMR Data-Utilized Multi-Scale Divide-and-Conquer Molecular Dynamics Simulation

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Structural and thermodynamic insights into antibody light chain tetramer formation through 3D domain swapping

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Computational Analysis Reveals a Critical Point Mutation in the N-Terminal Region of the Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with Canine Distemper Vir...

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GPNMB is a novel binding partner of FGFR1 that affects tumorigenic potential through AKT phosphorylation in TNBC

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Lichen-Derived Diffractaic Acid Inhibited Dengue Virus Replication in a Cell-Based System

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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

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Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography

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