Výsledky vyhledávání - "Yoshio Okiyama"

Akademický článek

Towards good correlation between fragment molecular orbital interaction energies and experimental IC50 for ligand binding: A case study of p38 MAP kinase

Autor: Yinglei Sheng, Hirofumi Watanabe, Keiya Maruyama, Chiduru Watanabe, Yoshio Okiyama, Teruki Honma, Kaori Fukuzawa, Shigenori Tanaka

Publikováno v: Computational and Structural Biotechnology Journal, Vol 16, Iss , Pp 421-434 (2018)

We describe several procedures for the preprocessing of fragment molecular orbital (FMO) calculations on p38 mitogen-activated protein (MAP) kinase and discuss the influence of the procedures on the protein–ligand interaction energies represented b

Externí odkaz: https://doaj.org/article/b27d0e33ee924923855840d31979ccc5

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Quantum Chemical Interaction Analysis between SARS-CoV-2 Main Protease and Ensitrelvir (Xocova) Compared with Its Initial Screening Hit

Autor: Chiduru Watanabe, Shigenori Tanaka, Yoshio Okiyama, Hitomi Yuki, Tatsuya Ohyama, Kikuko Kamisaka, Daisuke Takaya, Kaori Fukuzawa, Teruki Honma

A non-covalent oral drug targeting severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) main protease (Mpro), ensitrelvir (brand name Xocova), has been developed by Unoh et al. (J. Med. Chem. 2022, 65, 9, 6499–6512) using structure-based dr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::1092026b76b6be8c6f7183c157da27a3
https://doi.org/10.26434/chemrxiv-2022-drwc0

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In silico modeling of PAX8-PPAR gamma fusion protein in thyroid carcinoma: influence of structural perturbation by fusion on ligand-binding affinity

Autor: Yoshio Okiyama, Shigenori Tanaka, Kaori Sakaguchi

Publikováno v: Journal of Computer-Aided Molecular Design. 35(5):629-642

Paired box 8 (PAX8)-peroxisome proliferator-activated receptor γ (PPARγ) rearrangement is believed to play an important role in tumorigenesis of PAX8-PPARγ fusion protein (PPFP) thyroid carcinomas, while without establishing any standard treatment

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8ba9843725aa1c99f8827213987064cd
https://hdl.handle.net/20.500.14094/90008310

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FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method

Autor: Shunpei Nagase, Hitomi Yuki, Noriyuki Kurita, Teruki Honma, Shigenori Tanaka, Daisuke Takaya, Kikuko Kamisaka, Yoshio Okiyama, Midori Takimoto-Kamimura, Hirotomo Moriwaki, Yoichiro Yagi, Tatsuya Takagi, Norihito Kawashita, Kenichiro Takaba, Tomohiro Sato, Tomonaga Ozawa, Chiduru Watanabe, Kaori Fukuzawa

Publikováno v: Journal of Chemical Information and Modeling. 61:777-794

We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://dru

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::975e8c11a154591f0f90c0bdf4cd759a
https://doi.org/10.1021/acs.jcim.0c01062

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Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital (FMO) Method

Autor: Chiduru Watanabe, Yoshio Okiyama, Katsunori Segawa, Kaori Fukuzawa, Yuto Komeiji, Tatsuya Nakano, Yuji Mochizuki

Publikováno v: Bulletin of the Chemical Society of Japan. 94:91-96

The calculation speed of the ab initio fragment molecular orbital (FMO) method can and must be increased by applying approximations to the environmental electrostatic potential (ESP) and the dimer ...

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::2add7fd3de5f3854c6f2887dd848944b
https://doi.org/10.1246/bcsj.20200227

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Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7)

Autor: Yoshio Okiyama, Koji Okuwaki, Kaori Fukuzawa, Yuma Handa, Shigenori Tanaka, Ryo Hatada, Yuto Komeiji, Yuji Mochizuki

Publikováno v: Journal of Chemical Information and Modeling

The worldwide spread of COVID-19 (new coronavirus found in 2019) is an emergent issue to be tackled. In fact, a great amount of works in various fields have been made in a rather short period. Here, we report a fragment molecular orbital (FMO) based

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bf10d512e5c462bbe82f166ef4fd76ab
https://doi.org/10.1021/acs.jcim.0c00283

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New SIRT2 inhibitors: Histidine-based bleomycin spin-off

Autor: Halil I. Ciftci, Akihiro Ito, Ryoko Koga, Mikako Fujita, Akiko Nakata, Yoshio Okiyama, Taha F.S. Ali, Takeo Ohsugi, Minoru Yoshida, Masami Otsuka, Teruki Honma, Mohamed O. Radwan

Publikováno v: Bioorganic & Medicinal Chemistry. 27:1767-1775

Bleomycin is considered to exert its antitumor activity via DNA cleavage mediated by activated oxygen generated from the iron complex in its chelator moiety. Spin-offs from this moiety, HPH-1Trt and HPH-2Trt, with anti-cancer activities were recently

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9220b55d3344a28cd5acf9d0160105eb
https://doi.org/10.1016/j.bmc.2019.03.003

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