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量子生命情報薬学分野へようこそ

About

量子生命情報薬学分野について

About Quantum life science and bioinformatics

研究テーマ

Research Topics

生命科学現象は、それを構成する分子の挙動と分子間の相互作用から成り立っており、分子構造に基づく作用メカニズムの議論はあらゆる現象解明の基礎になります。コンピュータが発達した現代においては、計算科学を用いることによって分子の挙動を明らかにし、実験科学と相補的に新たな知見を生み出すことができます。当研究室では、量子化学計算を基軸として、物理化学の基本法則に則ってタンパク質や核酸、脂質などの生体高分子の動的挙動を原子分子レベルで明らかにし、生命科学現象の解明や創薬分子設計につなげる研究を行っています。また、スーパーコンピューター「富岳」を活用したデータ基盤の整備や人工知能(AI)の活用によって、量子化学に基づく生命科学研究のデジタルトランスフォーメーション(DX)の実現を目指しています。

  • 量子化学計算を用いた構造生命科学研究

    日本発の量子化学計算手法であるフラグメント分子軌道(FMO)法を用いて、薬物とタンパク質(受容体など)の結合性予測やタンパク質―タンパク質間相互作用解析、RNAなど核酸系、脂質膜と膜タンパク質の融合シミュレーション等を幅広く行い、構造生物学などの実験研究者と連携して研究を進めています。 FMO法は、タンパク質全体を量子化学的に扱い、電子的な効果も含めて分子複合体の相互作用を定量的に評価し、そのエネルギー成分から相互作用の性質を議論する事ができる世界最先端の手法です。 本研究室では、産学官連携の「FMO創薬コンソーシアム」(https://fmodd.jp)を主宰し、100名を超える創薬研究者とともに日々、FMO法を創薬技術として実用化するための研究開発を行っています。 スーパーコンピューター「富岳」の利用によって、これら量子化学計算データの取得を加速し、独自のデータベースである「FMOデータベース」(https://drugdesign.riken.jp/FMODB/)を整備し、今後のデータ駆動型研究の基盤構築と世界に向けた情報発信を行っています。

  • インシリコ創薬による医薬品候補化合物探索及び設計

    理論創薬分野では、主に創薬プロセスの探索研究段階で、薬物候補化合物の設計や予測を計算機上で行います。 基本となる考え方は、既存のリガンド分子の物性や構造情報に注目するLigand-Based Drug Design (LBDD)、ターゲットとなるタンパク質等の立体構造相補性に注目するStructure-Based Drug Design (SBDD)があります。 これらの基本的考え方を理解しつつ、実際のターゲット分子を制御する分子を計算機上で探索します。 LBDD及びSBDDには多くの方法論が提唱されており、現在でも新規手法の提案が活発に行われています。 また近年大量データから学習するAIによる手法も多く報告されています。 本研究室では広く使われている既存の手法に加えて、より精度の良い新規の医薬品設計手法開発のため、例えばFMO法の精密な相互作用エネルギーを記述子として大量に取り込む事で予測精度向上を目指しています。

  • 医薬品の効果・副作用分析、疫学調査、ソフトウェア開発

    医薬品の効果及び安全性は薬の臨床応用において極めて重要な課題です。また、医薬品の使用状況や感染症発生時の社会意識などは患者だけでなく、医療を提供する側にも注目すべきポイントです。 本研究室では、臨床試験の結果のメタアナリシスやcost-effectモデルの構築、副作用データベースのマイニング等を行っています。また、使いやすいソフトウェアやツールの開発にも取り組んでいます。

専任教員/Full-time Researchers

博士後期学生/PhD students

学部生/Undergraduate students

年間論文数/Yearly publications (2021)

Members

量情の チームメンバー

Team Members

福澤 薫 教授

Professor
Kaori Fukuzawa, Ph.D.
Email: fukuzawa-k
(@)phs.osaka-u.ac.jp

高谷 大輔 特任講師

Specially Appointed Lecturer
Daisuke Takaya, Ph.D.
Email: takaya-d
(@)phs.osaka-u.ac.jp

田 雨時 助教

Assistant Professor
Yu-Shi Tian, Ph.D.
Email: yushi-tian
(@)phs.osaka-u.ac.jp

牛尾 律子 秘書

Secretary
Ritsuko Ushio
Email: ushio-r
(@)office.osaka-u.ac.jp

学生

Students

博士後期学生 / PhD student
半田 佑磨 / Yuma Handa

6年生 / 6th grade student
里園 基裕 / Motohiro Satozon

3年生 / 3rd grade student
大野 修 / Shu Ono
白川 純一 / Junichi Shirakawa
田中 蒼大 / Sota Tanaka
宮岸 澄真 / Toma Miyagishi

Research Activities

研究業績

各メンバーの業績はメンバー欄にあるリンク先を参照ください.

学術論文

2022年度

  • Kenichiro Takaba, Chiduru Watanabe, Atsushi Tokuhisa, Yoshinobu Akinaga, Biao Ma, Ryo Kanada, Mitsugu Araki, Yasushi Okuno, Yusuke Kawashima, Hirotomo Moriwaki, Norihito Kawashita, Teruki Honma, Kaori Fukuzawa, and Shigenori Tanaka, "Protein–Ligand Binding Affinity Prediction of CDK2 Inhibitors by Dynamically Averaged FMO-based Interaction Energy", J. Comp. Chem., 43, 1362-1371 (2022). DOI: 10.1002/jcc.26940.
  • Jia Shi, Riku Kanoya, Yurina Tani, Sodai Ishikawa, Rino Maeda, Sana Suzuki, Fumiya Kawanami, Naoko Miyagawa, Katsuhiko Takahashi, Teruaki Oku, Ami Yamamoto, Kaori Fukuzawa, Motowo Nakajima, Tatsuro Irimura, and Nobuaki Higashi "Sulfated Hyaluronan Binds to Heparanase and Blocks Its Enzymatic and Cellular Actions in Carcinoma Cells" Int. J. Mol. Sci., 23, 5055 (2022). Int. J. Mol. Sci., 23, 5055 (2022). https://doi.org/10.3390/ijms23095055
  • Koh Takeuchi, Yoshiki Ikeda, Miki Senda, Ayaka Harada, Koji Okuwaki, Kaori Fukuzawa, So Nakagawa, Hong yang Yu, Lisa Nagase, Misaki Imai, Mika Sasaki, Yu-Hua Lo, Doshun Ito, Natsuki Osaka, Yuki Fujii, Atsuo T. Sasaki, and Toshiya Senda" The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity" Structure, 30, 1-14 (2022). https://doi.org/10.1016/j.str.2022.04.004
  • Kazue Inaba, Kana Ebihara, Miki Senda, Ryunosuke Yoshino, Chisako Sakuma, Kotaro Koiwai, Daisuke Takaya, Chiduru Watanabe, Akira Watanabe, Yusuke Kawashima, Kaori Fukuzawa, Riyo Imamura, Hirotatsu Kojima, Takayoshi Okabe, Nozomi Uemura, Shinji Kasai, Hirotaka Kanuka, Takashi Nishimura, Kodai Watanabe, Hideshi Inoue, Yuuta Fujikawa, Teruki Honma, Takatsugu Hirokawa, Toshiya Senda, Ryusuke Niwa, "Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti", BMC Biology, 2022, 20, 43. https://doi.org/10.1186/s12915-022-01233-2
  • Xiaohan Ma, Kenjirou Higash, Kaori Fukuzawa, Keisuke Ueda, Kazunori Kadota, Yuichi Tozuka, Etsuo Yonemochi, Kunikazu Moribe. "Computational approach to elucidate the formation and stabilization mechanism of amorphous formulation using molecular dynamics simulation and fragment molecular orbital calculation" International Journal of Pharmaceutics, 615, 121477 (2022). https://doi.org/10.1016/j.ijpharm.2022.121477
  • Koji Okuwaki, Kazuki Akisawa, Ryo Hatada, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji and Shigenori Tanaka, "Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method" Appl. Phys. Express 15, 017001 (2022). https://doi.org/10.35848/1882-0786/ac4300
  • Kaori Fukuzawa and Shigenori Tanaka, "Fragment Molecular Orbital Calculations for Biomolecules" Curr. Opin. Struct. Biol, 72, 127-134 (2022). https://doi.org/10.1016/j.sbi.2021.08.010
  • Takaaki Tatsuguchi, Takehito Uruno, Yuki Sugiura, Kounosuke Oisaki, Daisuke Takaya, Daiji Sakata, Yoshihiro Izumi, Takaya Togo, Yuko Hattori, Kazufumi Kunimura, Testuya Sakurai, Teruki Honma, Takeshi Bamba, Masafumi Nakamura, Motomu Kanai, Makoto Suematsu, Yoshinori Fukui, "Pharmacological intervention of cholesterol sulfate-mediated T cell exclusion promotes antitumor immunity" Biochemical and Biophysical Research Communications, 609, 183-188 (2022). https://doi.org/10.1016/j.bbrc.2022.04.035
  • Martin, Yi Zhou, Tatsuya Takagi, Yu-Shi Tian, "Safety, efficacy, and cost-effectiveness of insulin degludec U100 versus insulin glargine U300 in adults with type 1 diabetes: a systematic review and indirect treatment comparison" International Journal of Clinical Pharmacy, (2022). https://doi.org/10.1007/s11096-022-01410-x.

2021年度

  • 内海 洋平,梅田 大貴,奥脇 弘次,小畑 繁昭, 中山 尚史,後藤 仁志,古石 誉之,福澤 薫,米持 悦生「FMO結晶エネルギーを用いた結晶構造予測の高精度化―Target XXIIIを例として―」 J. Comput. Chem. Jpn, 20, 92-93 (2021). https://doi.org/10.2477/jccj.2021-0041
  • 半田 千彰, 小沢 知永, 福澤 薫, 米持 悦生「化合物のAmes予測におけるGraph Convolutional Networkの特徴評価」 J. Comp. Chem. Jpn, 20, 1-9 (2021). https://doi.org/10.2477/jccj.2020-0015
  • Kaori Fukuzawa, Koichiro Kato, Chiduru Watanabe, Yusuke Kawashima, Yuma Handa, Ami Yamamoto, Kazuki Watanabe, Tatsuya Ohyama, Kikuko Kamisaka, Daisuke Takaya, Teruki Honma, "Special Feature of COVID-19 in FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2 Related Proteins" J. Chem. Info. Model. 61, 4594-4612 (2021). https://doi.org/10.1021/acs.jcim.1c00694
  • Shigenori Tanaka, Shusuke Tokutomi, Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, and Yuji Mochizuki "Dynamic Cooperativity of Ligand–Residue Interactions Evaluated with the Fragment Molecular Orbital Method" J. Phys. Chem. B, 125, 6501–6512 (2021) https://doi.org/10.1021/acs.jpcb.1c03043
  • Agata Ishikawa, Hiroshi Takasaki, Atsushi Sakurai, Takuma Katayama, Koichi Wada, Takayuki Furuishi, Kaori Fukuzawa, Yasuko Obata, Etsuo Yonemochi "Manufacturability and Properties of Granules and Tablets Using the Eco-Friendly Granulation Method Green Fluidized Bed Granulation Compared to Direct Compression" Chem. Pharm. Bull., 69, 447-455 (2021). https://doi.org/10.1248/cpb.c20-00970
  • Kazuki Watanabe, Chiduru Watanabe, Teruki Honma, Yu-Shi Tian, Yusuke Kawashima, Norihito Kawashita, Kaori Fukuzawa, Tatsuya Takagi "Computational ab initio interaction analyses between neutralizing antibody and SARS-CoV-2 variant spike proteins using the fragment molecular orbital method" Bull Chem Soc Jpn, 94, 1794-1798 (2021). https://doi.org/10.1246/bcsj.20210104
  • Kazuki Watanabe, Chiduru Watanabe, Teruki Honma, Yu-Shi Tian, Yusuke Kawashima, Norihito Kawashita, Tatsuya Takagi, Kaori Fukuzawa "Intermolecular Interaction Analyses on SARS-CoV-2 Spike Protein Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/Peptide Using Fragment Molecular Orbital Calculation" J. Phys. Chem. Lett., 12, 4059–4066 (2021). https://doi.org/10.1021/acs.jpclett.1c00663.
  • Chisa Aoki, Xiaohan Ma, Kenjirou Higashi, Yuya Ishizuka, Keisuke Ueda, Kazunori Kadota, Kaori Fukuzawa, Yuichi Tozuka, Kohsaku Kawakami, Etsuo Yonemochi, Kunikazu Moribe "Stabilization mechanism of amorphous carbamazepine by transglycosylated rutin, a non-polymeric amorphous additive with a high glass transition temperature" International Journal of Pharmaceutics, 600, 120491-120501 (2021) https://doi.org/10.1016/j.ijpharm.2021.120491.
  • Majid Ismail Tamboli, Yushi Okamoto, Yohei Utsumi, Takayuki Furuishi, Siran Wang, Daiki Umeda, Okky Dwichandra Putra, Kaori Fukuzawa, Hidehiro Uekusa, Etsuo Yonemochi "Crystal Structures of Antiarrhythmic Drug Disopyramide and Its Salt with Phthalic Acid" Crystals 11, 379 - 379 (2021).
  • Majid Ismail Tamboli, Yohei Utusmi, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi "Crystal Structure of Novel Terephthalate Salt of Antiarrhythmic Drug Disopyramide" Crystals 11, 368-368 (2021).
  • Chiduru Watanabe, Yoshio Okiyama, Shigenori Tanaka, Kaori Fukuzawa, Teruki Honma, "Molecular Recognition of SARS-CoV-2 Spike Glycoprotein: Quantum Chemical Hot Spot and Epitope Analyses" Chem. Sci. 12, 4722- (2021). https://doi.org/10.1039/D0SC06528E
  • Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki*, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka. "Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations" RSC Advances 11, 3272-3279 (2021). https://doi.org/10.1039/D0RA09555A
  • Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka "Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation" Applied Physics Express 14, 027003 - 027003 (2021). https://doi.org/10.35848/1882-0786/abdac6
  • Daisuke Takaya, Chiduru Watanabe, Shunpei Nagase, Kikuko Kamisaka, Yoshio Okiyama, Hirotomo Moriwaki, Hitomi Yuki, Tomohiro Sato, Noriyuki Kurita, Yoichiro Yagi, Tatsuya Takagi, Norihito Kawashita, Tomonaga Ozawa, Midori Takimoto-Kamimura, Shigenori Tanaka, Kaori Fukuzawa, Teruki Honma" FMODB: The world's first database of quantum mechanical calculation for biomacromolecules based on the fragment molecular orbital method" J. Chem. Info. Model., 61, 777-794 (2021). https://doi.org/10.1021/acs.jcim.0c01062
  • Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuto Komeiji, Katsunori Segawa, Yuji Mochizuki "Acceleration of environmental electrostatic potential using Cholesky decomposition with adaptive metric (CDAM) for fragment molecular orbital (FMO) method" Bul. Chem. Soc. J., 94, 91-96 (2021). https://doi.org/10.1246/bcsj.20200227
  • Hiroyuki Yoshida, Keita Teruya, Yasuhiro Abe, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi, Ken-ichi Izutsu, "Altered Media Flow and Tablet Position as Factors of How Air Bubbles Affect Dissolution of Disintegrating and Non-disintegrating Tablets Using a USP 4 Flow-Through Cell Apparatus", AAPS PHARMSCITECH, 22(7), (2021). https://doi.org/10.1208/s12249-021-02117-4
  • Tatsuya Nakano, Tsuguchika Kaminuma, Toshiyuki Sato, Kaori Fukuzawa, Yutaka Akiyama, Masami Uebayasi, Kazuo Kitaura, "Fragment molecular orbital method: use of approximate electrostatic potential", Chemical Physics Letters 351 (5-6), 475-480, (2021). https://doi.org/10.1016/S0009-2614(01)01416-6
  • Kohei Fukuto, Tatsuya Takagi, Yu-Shi Tian, "Predicting the side effects of drugs using matrix factorization on spontaneous reporting database", Scientific reports, 11(1) 23942-23942, (2021). https://doi.org/10.1038/s41598-021-03348-y
  • Martin, Yi Zhou, Tatsuya Takagi, Yu-Shi Tian, "Efficacy and safety among second-generation and other basal insulins in adult patients with type 1 diabetes: a systematic review and network meta-analysis", Naunyn-Schmiedeberg's Archives of Pharmacology, 394(10) 2091-2101, (2021). https://doi.org/10.1007/s00210-021-02128-9
  • Yusuke Kawashima, Natsumi Mori, Norihito Kawashita, Yu-Shi Tian, Tatsuya Takagi, "Combining self-organizing maps and hierarchical clustering for protein–ligand interaction analysis in post-fragment molecular orbital calculation", Chem-Bio Informatics Journal, 2021, 21, 1-10. https://doi.org/10.1273/cbij.21.1

2020年度

  • Shusuke Tokutomi, Kohei Shimamura, Kaori Fukuzawa and Shigenori Tanaka "Machine learning prediction of inter-fragment interaction energies between ligand and amino-acid residues on the fragment molecular orbital calculations for Janus kinase–inhibitor complex" Chem. Phys. Lett., 757, 137883-137890 (2020). https://doi.org/10.1016/j.cplett.2020.137883
  • Koichiro Kato, Teruki Honma, Kaori Fukuzawa "Intermolecular Interaction Among Remdesivir, RNA and RNA-Dependent RNA Polymerase of SARS-CoV-2 Analyzed by Fragment Molecular Orbital Calculation" J. Mol. Graph. Model., 100, 107695-107699 (2020). https://doi.org/10.1016/j.jmgm.2020.107695
  • Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, and Shigenori Tanaka "Fragment molecular orbital based interaction analyses on COVID-19 main protease - inhibitor N3 complex (PDB ID:6LU7)" J. Chem. Info. Model., 60, 3593-3602 (2020). https://dx.doi.org/10.1021/acs.jcim.0c00283.
  • Koichiro Kato, Tomohide Masuda*, Chiduru Watanabe*, Naoki Miyagawa, Hideo Mizouchi, Shumpei Nagase, Kikuko Kamisaka, Kanji Oshima, Satoshi Ono, Hiroshi Ueda, Atsushi Tokuhisa, Ryo Kanada, Masateru Ohta, Mitsunori Ikeguchi, Yasushi Okuno, Kaori Fukuzawa, and Teruki Honma "High-precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning" J. Chem. Info. Model., 60, 3361-3368 (2020). https://dx.doi.org/10.1021/acs.jcim.0c00273.
  • Shigenori Tanaka, Chiduru Watanabe, Teruki Honma, Kaori Fukuzawa, Kazue Ohishi, and Tadashi Maruyama "Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method" J. Mol. Graph. Model., 100, 107650-107662 (2020). https://doi.org/10.1016/j.jmgm.2020.107650
  • Hiroki Tanaka, Tatsunari Takahashi, Manami Konishi, Nae Takata, Masaki Gomi, Daiki Shirane, Yuki Yamasaki, Yu Sakurai, Keisuke Ueda, Kenjirou Higashi, Kunikazu Mroibe, Eiji Shinsho, Ruka Nishida, Kaori Fukuzawa, Etsuo Yonemochi, Koji Okuwaki, Yuji Mochizuki, Yuta Nakai, Kota Tange, Hiroki Yoshioka, Shinya Tamagawa, Hidetaka Akita, "Self‐Degradable Lipid‐Like Materials Based on "Hydrolysis accelerated by the intra‐Particle Enrichment of Reactant (HyPER)" for Messenger RNA Delivery" Advanced Functional Materials, 1910575 (2020) https://doi.org/10.1002/adfm.201910575.
  • 畑田崚, 加藤幸一郎, 奥脇弘次, 福澤薫, 望月 祐志 「カルサイト・ハイドロキシアパタイト結晶表面とペプチドの FMO相互作用解析」J. Comput. Chem. Jpn., 19, 1-7 (2020). https://doi.org/10.2477/jccj.2019-0030. Ryo Hatada, Kouichiro Kato, Koji Okuwaki, Kaori Fukuzawa, Yuji Mochizuki "Interaction Analyses between Calcite/Apatite and Peptides by Fragment Molecular Orbital Method.".
  • Yoshinobu Akinaga, Koichiro Kato, Tatsuya Nakano, Kaori Fukuzawa, Yuji Mochizuki "Fragmentation at sp2 carbon in fragment molecular orbital (FMO) method" J. Comput. Chem, 41, 1416-1420 (2020); DOI: 10.1002/jcc.26190.
  • Nanami Hata, Takayuki Furuishi, Majid I. Tamboli, Momiji Ishizaki, Daiki Umeda, Kaori Fukuzawa and Etsuo Yonemochi "Crystal Structural Analysis of DL-Mandelate Salt of Carvedilol and Its Correlation with Physicochemical Properties" Crystals 10, 53 (2020). https://doi.org/10.3390/cryst10010053.
  • Kotaro Koiwai, Kazue Inaba, Kana Morohashi, Sora Enya, Reina Arai, Hirotatsu Kojima, Takayoshi Okabe, Yuuta Fujikawa, Hideshi Inoue, Ryunosuke Yoshino, Takatsugu Hirokawa, Koichiro Kato, Kaori Fukuzawa, Yuko Shimada-Niwa, Akira Nakamura, Fumiaki Yumoto, Toshiya Senda, Ryusuke Niwa "An integrated approach unravels a crucial structural property for the function of the insect steroidogenic Halloween protein Noppera-bo" J. Biol. Chem., 295, 7154-7167 (2020). https://doi.org/10.1074/JBC.RA119.011463
  • Koji Okuwaki, Hideo Doi, Kaori Fukuzawa, Yuji Mochizuki, "Folding simulation of small proteins by dissipative particle dynamics (DPD) with non-empirical interaction parameters based on fragment molecular orbital calculations" Applied Physics Express (APEX), 13, 017002 (2020). https://doi.org/10.7567/1882-0786/ab5e0a
  • Yuji MOCHIZUKI, Kota SAKAKURA, Hiromasa WATANABE, Koji OKUWAKI, Koichiro KATO, Naoki WATANABE, Yoshio OKIYAMA, Kaori FUKUZAWA, Tatsuya NAKANO, "Development Status of ABINIT-MP in 2020" Journal of Computer Chemistry, 19(4), 142-145 (2020). https://doi.org/10.2477/jccj.2021-0015
  • Daisuke Takaya, Hideaki Niwa, Junko Mikuni, Kana Nakamura, Noriko Handa, Akiko Tanaka, Shigeyuki Yokoyama, Teruki Honma, "Protein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method" JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 99, 107599-107599 (2020). https://doi.org/10.1016/j.jmgm.2020.107599
  • Mohamed O. Radwan, Daisuke Takaya, Ryoko Koga, Kana Iwamaru, Hiroshi Tateishi, Taha F. S. Ali, Akifumi Takaori-Kondo, Masami Otsuka, Teruki Honma, Mikako Fujita, "Interruption of Vif/Elongin C interaction: In silico and experimental elucidation of the underlying molecular mechanism of benzimidazole-based APOBEC3G stabilizers" BIOORGANIC & MEDICINAL CHEMISTRY, 28(8), 115409 (2020). https://doi.org/10.1016/j.bmc.2020.115409
  • Asuka Hatabu, Xinhua Mao, Yi Zhou, Norihito Kawashita, Zheng Wen, Mikiko Ueda, Tatsuya Takagi, Yu-Shi Tian, "Knowledge, attitudes, and practices toward COVID-19 among university students in Japan and associated factors: An online cross-sectional survey", PLOS ONE, 15(12) e0244350 (2020). https://doi.org/10.1371/journal.pone.0244350
  • Yi Zhou, Siu-wai Leung, Shosuke Mizutani, Tatsuya Takagi, Yu-Shi Tian, "MEPHAS: an interactive graphical user interface for medical and pharmaceutical statistical analysis with R and Shiny", BMC Bioinformatics, 21(1) 183-183 (2020). https://doi.org/10.1186/s12859-020-3494-x
  • Kazuki Watanabe, Yusuke Kawashima, Chisato Mukai, Tatsuya Takagi, Yukinori Suwa, Yu-Shi Tian, Norihito Kawashita, "A Comparison between the Cycloadditions of Allenyl- and Vinyl-Cyclopentanes Using Density Functional Theory and GRRM Program", Chemical and Pharmaceutical Bulletin, 68(8), 737-741 (2020). https://doi.org/10.1248/cpb.c20-00144
  • Martin, Yi Zhou, Chun-Xu Meng, Tatsuya Takagi, Yu-Shi Tian, "Vonoprazan vs proton pump inhibitors in treating post-endoscopic submucosal dissection ulcers and preventing bleeding: roton pump inhibitors in treating post-endoscopic submucosal dissection ulcers and preventing bleeding", Medicine, 99(9) e19357 (2020). doi: 10.1097/MD.0000000000019357

2019年度

  • Koichiro Kato, Kaori Fukuzawa, and Yuji Mochizuki "Interaction between calcite and adsorptive peptide analyzed by fragment molecular orbital method" Japanese Journal of Applied Physics 58, 120906 (2019). https://doi.org/10.7567/1347-4065/ab5335
  • 望月 祐志, 秋永 宜伸, 坂倉 耕太, 渡邊 啓正, 加藤 幸一郎, 渡辺 尚貴, 奥脇 弘次, 中野 達也, 福澤 薫「ABINIT-MP Openシリーズの最新の開発状況について」J. Comput. Chem. Jpn., 18 129-131 (2019). https://doi.org/10.2477/jccj.2019-0016.
  • 坂田 千夏, 岡本 有史, 梅田 大貴, 古石 誉之, 福澤 薫*, 米持 悦生 「実験と計算によるイルソグラジン—マレイン酸の結晶構造の予測」 J. Comput. Chem. Jpn., 18 156-157 (2019). DOI: https://doi.org/10.2477/jccj.2019-0024. Chinatsu Sakata, Yushi Okamoto, Daiki Umeda, Takayuki Furuishi, Kaori Fukuzawa*, Etsuo Yonemochi "Crystal structure prediction of irsogladine maleate by experimental and computational methods".
  • 中野達也, 望月祐志, 福澤薫, 沖山佳生, 渡邉千鶴 「Bond detached atom (BDA)を共有しているフラグメント間の相互作用エネルギーの補正に関する試みII:ラジカル開裂補正」J. Comput. Aid. Chem., 20, 1-6, (2019). Tatsuya Nakano, Yuji Mochizuki, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe "A Radical Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA)"
  • Chiduru Watanabe, Hirofumi Watanabe, Yoshio Okiyama, Daisuke Takaya, Kaori Fukuzawa, Shigenori Tanaka, Teruki Honma "Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical calculation database for large biomolecules" Chem-Bio Info. J., 19, 5-18 (2019). DOI: https://doi.org/10.1273/cbij.19.5
  • Andre' Rossberg, Takaya Abe, Koji Okuwaki, Astrid Barkleit, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki and Satoru Tsushima "Destabilization of DNA through interstrand crosslinking by UO22+" Chem. Commun., 55, 2015-2018 (2019). DOI: 10.1039/c8cc09329f
  • Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimir Sladek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu and Yasuteru Shigeta, "Development of an analysis toolkit, Analysis FMO, to visualize interaction energies generated by fragment molecular orbital calculations" J. Chem. Inf. Model., 59, 25-30 (2019). DOI: 10.1021/acs.jcim.8b00649.
  • Yoshio Okiyama, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka, "Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies" J. Phys. Chem. B, 123, 957–973 (2019). DOI: 10.1021/acs.jpcb.8b09326.
  • Takayuki Furuishi, Kohei Sekino, Mihoko Gunji, Kaori Fukuzawa, Hiromasa Nagase, Tomohiro Endo, Haruhisa Ueda, Etsuo Yonemochi, "Effect of sulfobutyl ether-β-cyclodextrin and propylene glycol alginate on the solubility of clozapine" Pharmaceutical Development and Technology, 2019, 24(4), 479-486. DOI: 10.1080/10837450.2018.1514521
  • Shintaro Iwasaki, Wakana Iwasaki, Mari Takahashi, Ayako Sakamoto, Chiduru Watanabe, Yuichi Shichino, Stephen N Floor, Koichi Fujiwara, Mari Mito, Kosuke Dodo, Mikiko Sodeoka, Hiroaki Imataka, Teruki Honma, Kaori Fukuzawa, Takuhiro Ito, Nicholas T Ingolia, "The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA" Molecular cell, 73(4), 738-748 (2019). https://doi.org/10.1016/j.molcel.2018.11.026
  • Hirotomo Moriwaki, Yu-Shi Tian, Norihito Kawashita, Tatsuya Takagi, "Three-Dimensional Classification Structure–Activity Relationship Analysis Using Convolutional Neural Network", Chemical and Pharmaceutical Bulletin, 67(5), 1-8 (2019). https://doi.org/10.1248/cpb.c18-00757
  • 岡良成, 田雨時, 幡生あすか, 高木達也, "小児を中心とした結核予防に対する BCG 効果の メタアナリシス分析" 日本小児臨床薬理学会雑誌, 32(1), 65-81 (2019).
  • Vonoprazan versus proton pump inhibitors in treating post-endoscopic submucosal dissection ulcers and preventing bleeding: Protocol for meta-analysis of randomized controlled trials and observational studies, Martin, Yi Zhou, Chun-Xu Meng, Tatsuya Takagi, Yu-Shi Tian, Medicine, 98(8), e14381 (2019). doi: 10.1097/MD.0000000000014381.

2018年度

  • 関 祐哉, 加藤 司, 古石 誉之, 福澤 薫*, 米持 悦生「FMO法によるエストロゲン受容体のリガンド結合特異性解析」J. Comput. Chem. Jpn., 17, 160-162 (2018). DOI: 10.2477/jccj.2018-0028. Yuya Seki, Tsukasa Kato, Takayuki Furuishi, Kaori Fukuzawa*, Etsuo Yonemochi "Analysis of ligand binding specificity of estrogen receptor by the fragment molecular orbital method"
  • Yinglei Sheng, Hirofumi Watanabe, Keiya Maruyama, Chiduru Watanabe, Yoshio Okiyama, Teruki Honma, Kaori Fukuzawa, Shigenori Tanaka "Toward good correlation between FMO interaction energies and experimental IC50 for ligand binding: A case study of p38 MAP kinase" Computational and Structural Biotechnology Journal,16, 421-434 (2018). https://doi.org/10.1016/j.csbj.2018.10.003
  • Tatsuya Nakano, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe, Yuto Komeiji, Yuji Mochizuki, "Accuracy of Dimer-ES Approximation on Fragment Molecular Orbital (FMO) Method Chem-Bio Info. J., 18, 119-122 (2018). https://doi.org/10.1273/cbij.18.119
  • Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa "Interaction between a single-stranded DNA and a binding protein viewed by the fragment molecular orbital method" Bull. Chem. Soc. Jpn., 91, 1596-1605 (2018), doi:10.1246/bcsj.20180150.
  • 新庄 永治, 奥脇 弘次, 土居 英男, 望月 祐志, 古石 誉之, 福澤 薫, 米持 悦生 「X線小角散乱と散逸粒子動力学法を用いた脂質膜およびベシクル形成メカニズムの解明」Eiji Shinsho, Koji Okuwaki, Hideo Doi, Yuji Mochizuki, Takayuki Furuishi, Kaori Fukuzawa*, and Etsuo Yonemochi, "Formation mechanism of lipid membrane and vesicle using small angle X-ray scattering and dissipative particle dynamics (DPD) method", J. Comput. Chem. Jpn, 17, 172-179 (2018). https://doi.org/10.2477/jccj.2018-0012
  • Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki and Shigenori Tanaka "Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: Implementation and DNA Study" J. Phys Chem. B, 122, 4457-4471 (2018). DOI: 10.1021/acs.jpcb.8b01172
  • Keiya Maruyama; Yinglei Sheng; Hirofumi Watanabe, Kaori Fukuzawa, Shigenori Tanaka "Application of singular value decomposition to the inter-fragment interaction energy analysis for ligand screening" Comp. Theor. Chem, 1132, 23-34 (2018). https://doi.org/10.1016/j.comptc.2018.04.001
  • 奥脇弘次, 土居英男, 望月祐志, 小沢拓, 泰岡顕治, 福澤薫, "FMO計算-粗視化シミュレーション連携手法の開発と応用", J. Comp. Chem. Jpn. 17, 144-146 (2018).Development and Application of FMO Calculation − DPD Simulation Conbination Scheme, Okuwaki Koji, Doi Hideo, Mochizuki Yuji, Ozawa Taku, Yasuoka Kenji, Fukuzawa Kaori, Journal of Computer Chemistry, Japan, 17(3), 144 (2018).
  • Daisuke Takaya, Koji Inaka, Akifumi Omura, Kenji Takenuki, Masashi Kawanishi, Yukako Yabuki, Yukari Nakagawa, Keiko Tsuganezawa, Naoko Ogawa, Chiduru Watanabe, Teruki Honma, Kosuke Aritake, Yoshihiro Urade, Mikako Shirouzu, Akiko Tanaka, "Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies" BIOORGANIC & MEDICINAL CHEMISTRY, 26(16), 4726-4734 (2018). https://doi.org/10.1016/j.bmc.2018.08.014
  • Hirotomo Moriwaki, Yu-Shi Tian, Norihito Kawashita, Tatsuya Takagi, Mordred: A molecular descriptor calculator, Journal of Cheminformatics, 10(1), 4 (2018). https://doi.org/10.1186/s13321-018-0258-y
  • Yu-Shi Tian, Yi Zhou, Tatsuya Takagi, Masanori Kameoka, Norihito Kawashita, Dengue virus and its inhibitors: A brief review, Chemical and Pharmaceutical Bulletin, 66(3), 191-206 (2018). https://doi.org/10.1248/cpb.c17-00794

学会発表

2022年度

  • TBD

著書

  • "Recent Advances of the Fragment Molecular Orbital Method" ed. by Yuji Mochizuki, Shigenori Tanaka and Kaori Fukuzawa, Springer Nature, (2021). https://doi.org/10.1007/978-981-15-9235-5.
  • Yoshio Okiyama, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka "Taking Water into Account with the Fragment Molecular Orbital Method" in "Quantum Mechanics in Drug Discovery" edited by Alexander Heifetz (Springer Nature, 2020) pp. 105-122. https://doi.org/10.1007/978-1-0716-0282-9
  • Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka "Application of FMO method to specific molecular recognition of biomacromolecules" in "The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems" edited by D. G. Fedorov and K. Kitaura (Taylor & Francis/ CRC Press, Boca Raton, FL, 2009), pp. 133-170.
  • 佐藤文俊、中野達也、望月祐志 編著“プログラムで実践する生体分子量子化学計算” (森北出版、東京、2008)
  • 中野達也、谷森奏一郎、加藤昭史、小池上繁、雨宮克樹、福澤薫 “フラグメント分子軌道法入門‐ABINIT-MPによるタンパク質の非経験的量子化学計算‐”,(アドバンスソフト株式会社、東京、2004)
  • In silico創薬におけるスクリーニングの高速化・効率化技術, 福澤 薫 (担当:分担執筆, 範囲:スーパーコンピュータを用いたFMO研究の実際), 技術情報協会.

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