TRAN DUY PHUOC

論文

• ADP-Bound States of Cytoplasmic Dynein: Cryo-electron Microscopy Reveals a Two-Step Post-Power-Stroke Transition and Roles of Regulatory ATPase Sites

  Hiroshi Imai, Riko Kanazawa, Toshihisa Maeshima, Duy Phuoc Tran, Rieko Shimo-Kon, Hisaya Tokita, Tomoko Miyata, Fumiaki Makino, Junso Fujita, Takayuki Kato …

  Journal of Molecular Biology 169977-169977 2026年8月 査読有り
• Mechanistic insight into signal bias by the agonist-dependent conformational dynamics of GPR84

  Shota Suzuki, Duy Phuoc Tran, Kouki Nishikawa, Akio Kitao, Yoshinori Fujiyoshi

  Nature Communications 2026年7月16日 査読有り
• DRD1-driven infantile dystonia: towards a mechanism-informed framework for GPCR receptoropathies

  Gülsüm Kayhan, Ryosuke Tany, Reza Maroofian, Esra Serdaroğlu, Eon Kurumiya, Duy Phuoc Tran, Hideko Wakasugi-Masuho, Mirja Thomsen, Kamran Salayev, Rauan Kaiyrzhanov …

  Brain 2026年4月9日 査読有り
• In Vitro Evolution of the Adenosine A _2A Receptor Based on an Antagonist Binding Using a Ribosome Display

  Genki Fukasawa, Yuma Matsuoka, Duy Phuoc Tran, Haruka Nishigaki, Keisuke Fukunaga, Takayoshi Watanabe, Tomohiro Doura, Naohiro Terasaka, Ako Kagawa, Takeshi Murata …

  Journal of the American Chemical Society 148(10) 11415-11423 2026年3月6日 査読有り
• The role of the tryptophan-rich allosteric network and sodium egress in GPCR activation

  Zhenzhou Qi, Duy Phuoc Tran, Andrejs Tučs, Roopan Thiara, Louis-Philippe Picard, Koji Tsuda, Aditya Pandey, Adnan Sljoka, Akio Kitao, Robert Scott Prosser

  Proceedings of the National Academy of Sciences 123(10) 2026年3月3日 査読有り筆頭著者
• Revisiting Vacuum Simulations Using Modern Classical Protein Force Fields

  Vi Toan Lam, Duy Phuoc Tran

  ACS Omega 11(5) 7464-7474 2026年1月28日 査読有り最終著者責任著者
• Single layer graphene flake transformation from flat to convex

  Phuc Vu Le, Phi Minh Nguyen, Hoa Van Nguyen, Vi Toan Lam, Hanh Thi-Thu Tran, Duy Phuoc Tran

  Discover Materials 6 56 2025年12月26日 査読有り最終著者責任著者
• Tandem Allosteric Effects of Reactant and Product that Promote Deacetylation Cycles in Sir2

  Zhen Bai, Duy Phuoc Tran, Akio Kitao

  Journal of Chemical Information and Modeling 65(20) 11326-11341 2025年10月13日 査読有り
• Shear-induced fibronectin fibrillogenesis: Differential mechanisms under high and low shear stress conditions

  Quang Phuc Le, Hoang Huy Mai, Thao Nghi Nguyen Hoang, Hanh Thu Thi Tran, Duy Phuoc Tran, Khon Huynh

  Archives of Biochemistry and Biophysics 771 110518-110518 2025年9月 査読有り責任著者
• Correction to: Balancing G protein selectivity and efficacy in the adenosine A2A receptor (Nature Chemical Biology, (2025), 21, 1, (71-79), 10.1038/s41589-024-01682-6)

  Picard, L.-P., Orazietti, A., Tran, D.P., Tucs, A., Hagimoto, S., Qi, Z., Huang, S.K., Tsuda, K., Kitao, A., Sljoka, A. …

  Nature Chemical Biology 21(1) 155-155 2025年 査読有り
• Balancing G protein selectivity and efficacy in the adenosine A2A receptor.

  Louis-Philippe Picard, Alexander Orazietti, Duy Phuoc Tran, Andrejs Tucs, Sari Hagimoto, Zhenzhou Qi, Shuya Kate Huang, Koji Tsuda, Akio Kitao, Adnan Sljoka …

  Nature chemical biology 21(1) 81-79 2024年7月31日 査読有り
• PaCS-Toolkit: Optimized Software Utilities for Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Simulations and Subsequent Analyses

  Shinji Ikizawa, Tatsuki Hori, Tegar Nurwahyu Wijaya, Hiroshi Kono, Zhen Bai, Tatsuhiro Kimizono, Wenbo Lu, Duy Phuoc Tran, Akio Kitao

  Journal of Physical Chemistry B 128(15) 3631-3642 2024年4月18日 査読有り
• Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein

  Mariko Kojima, Satoshi Abe, Tadaomi Furuta, Duy Phuoc Tran, Kunio Hirata, Keitaro Yamashita, Yuki Hishikawa, Akio Kitao, Takafumi Ueno

  Biomaterials Science 11(4) 1350-1357 2023年 査読有り
• Structure of MotA, a flagellar stator protein, from hyperthermophile

  Tatsuro Nishikino, Norihiro Takekawa, Duy Phuoc Tran, Jun-ichi Kishikawa, Mika Hirose, Sakura Onoe, Seiji Kojima, Michio Homma, Akio Kitao, Takayuki Kato …

  Biochemical and Biophysical Research Communications 631 78-85 2022年11月 査読有り筆頭著者
• Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer

  Duy Phuoc Tran, Yuta Taira, Takumi Ogawa, Ryoga Misu, Yoshiki Miyazawa, Akio Kitao

  Scientific Reports 12(1) 3860-3860 2022年4月 査読有り筆頭著者責任著者
• 解離並列カスケード選択分子動力学とマルコフ状態モデルを用いて計算したタンパク質/リガンド複合体の結合自由エネルギー

  Hata Hiroaki, Phuoc Tran Duy, Marzouk Sobeh Mohamed, Marzouk Sobeh Mohamed, Kitao Akio

  Biophysics and Physicobiology (Web) 18 305-316 2021年12月 査読有り筆頭著者
• Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides

  Duy Phuoc Tran, Seiichi Tada, Akiko Yumoto, Akio Kitao, Yoshihiro Ito, Takanori Uzawa, Koji Tsuda

  Scientific Reports 11(1) 10630-10630 2021年12月 査読有り筆頭著者
• Calculation of Binding Free Energy and Kinetic Rates with Flexible Protein Docking

  Duy Phuoc TRAN, Akio KITAO

  Seibutsu Butsuri 61(6) 398-399 2021年10月 査読有り招待有り筆頭著者
• Delineating the conformational landscape of the adenosine A2A receptor during G protein coupling

  Shuya Kate Huang, Aditya Pandey, Duy Phuoc Tran, Nicolas L. Villanueva, Akio Kitao, Roger K. Sunahara, Adnan Sljoka, R. Scott Prosser

  Cell 184(7) 1884-1894 2021年3月 査読有り
• Erratum: Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins (Journal of Chemical Physics (2020) 152 (225101) DOI: 10.1063/5.0004654)

  Kenichiro Takaba, Duy Phuoc Tran, Akio Kitao

  Journal of Chemical Physics 153(17) 179902-179902 2020年11月7日 査読有り