TRAN PHUOC DUY ＴＲＡＮＰＨＵＯＣ・ＤＵＹ

… Alternative Names

TRAN PHUOC・DUY チャンフ・ズイ

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Researcher Number	50848546
Other IDs
Affiliation (Current)	2025: 東京科学大学, 生命理工学院, 助教
Affiliation (based on the past Project Information) *help	2023 – 2024: 東京工業大学, 生命理工学院, 助教 2019 – 2020: 東京工業大学, 生命理工学院, 助教
Review Section/Research Field	Principal Investigator Basic Section 43040:Biophysics-related / 0701:Biology at molecular to cellular levels, and related fields Except Principal Investigator Basic Section 43040:Biophysics-related
Keywords	Principal Investigator PaCS-MD / Flagellar stator MotAB / Molecular dynamics / MotA/B / Flagellar motor stators / Markov State Model / MD simulation / DNA scanning / dissociation simulation / association simulation … More / kinetic rate calculation / eePaCS-MD / A2a receptor / p53 protein / koff / docking / IDP / p53 / a/dPaCS-MD … More Except Principal Investigator PaCS-MD/MSM / ハブタンパク質 / ユビキチン化 / メチル化 / リン酸化 Less

Investigating molecular interactions of p53 regulated by post translation modifications and intrinsically disordered regions with advanced simulation
- Principal Investigator
  
  北尾彰朗
- Project Period (FY)
  2023 – 2026
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  Institute of Science Tokyo
Ion permeation and rotation mechanisms in bacterial flagellar motor statorsPrincipal Investigator
- Principal Investigator
  
  TRAN PHUOC・DUY
- Project Period (FY)
  2023 – 2024
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  Tokyo Institute of Technology
Atomistic mechanism of the oligomerization of p53 protein in DNA scanningPrincipal Investigator
- Principal Investigator
  
  TRAN PHUOC DUY
- Project Period (FY)
  2019 – 2020
- Research Category
  
  Grant-in-Aid for Research Activity Start-up
- Review Section
  
  0701:Biology at molecular to cellular levels, and related fields
- Research Institution
  Tokyo Institute of Technology

All 2024 2023 2021 2020 2019

All Journal Article Presentation

[Journal Article] PaCS-Toolkit: Optimized Software Utilities for Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Simulations and Subsequent Analyses2024
- Author(s)
  Ikizawa Shinji、Hori Tatsuki、Wijaya Tegar Nurwahyu、Kono Hiroshi、Bai Zhen、Kimizono Tatsuhiro、Lu Wenbo、Tran Duy Phuoc、Kitao Akio
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 128 Issue: 15 Pages: 3631-3642
- DOI
  10.1021/acs.jpcb.4c01271
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K14154, KAKENHI-PUBLICLY-22H04745, KAKENHI-PUBLICLY-23H04058, KAKENHI-PROJECT-23K27117, KAKENHI-PROJECT-23K27138
[Journal Article] Delineating the conformational landscape of the adenosine A2A receptor during G protein coupling2021
- Author(s)
  Huang, S. K., Pandey, A., Tran, D. P., Villanueva, N. L., Kitao, A., Sunahara, R. K., Sljoka, A. and Prosser, R. S.
- Journal Title
  
  Cell
  
  Volume: 184 Issue: 7 Pages: 1884-1894.e14
- DOI
  10.1016/j.cell.2021.02.041
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-20H05439, KAKENHI-PROJECT-19H03191, KAKENHI-PROJECT-19K23721
[Journal Article] Generating Ampicillin-Level Antimicrobial Peptides with Activity-Aware Generative Adversarial Networks2020
- Author(s)
  Tucs Andrejs、Tran Duy Phuoc、Yumoto Akiko、Ito Yoshihiro、Uzawa Takanori、Tsuda Koji
- Journal Title
  
  ACS Omega
  
  Volume: 5 Issue: 36 Pages: 22847-22851
- DOI
  10.1021/acsomega.0c02088
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K23721
[Journal Article] PaCS-MD/MSM : Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method2020
- Author(s)
  Duy Phuoc Tran, Hata Hiroaki, Ogawa Takumi, Taira Yuta, Kitao Akio
- Journal Title
  
  アンサンブル : 分子シミュレーション研究会会誌
  
  Volume: 22 Pages: 151-156
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K23721
[Journal Article] Kinetic Selection and Relaxation of the Intrinsically Disordered Region of a Protein upon Binding2020
- Author(s)
  Tran Duy Phuoc、Kitao Akio
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 16 Issue: 4 Pages: 2835-2845
- DOI
  10.1021/acs.jctc.9b01203
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K23721, KAKENHI-PROJECT-19H03191
[Journal Article] Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins2020
- Author(s)
  Kenichiro Takaba, Duy Phuoc Tran and Akio Kitao
- Journal Title
  
  J. Chem. Phys.
  
  Volume: 152 Issue: 22 Pages: 225101-225101
- DOI
  10.1063/5.0004654
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-20H05439, KAKENHI-PROJECT-19H03191, KAKENHI-PROJECT-19K23721
[Presentation] べん毛モーター固定子MotA/Bタンパク質複合体のイオン透過シミュレーション(Simulating ion permeation through the flagellar motor stator MotA/B protein complexes)2024
- Author(s)
  Duy Phuoc Tran
- Organizer
  2023年度べん毛研究交流会
- Data Source
  KAKENHI-PROJECT-23K27138
[Presentation] Simulating ion permeation through the flagellar motor stator MotA/B protein complexes2024
- Author(s)
  Duy Phuoc Tran, Akio Kitao
- Organizer
  Flagellar Meeting 2023
- Data Source
  KAKENHI-PROJECT-23K14154
[Presentation] Unveiling the dynamics of Adenosine A2a receptor coupling to the G proteins: a molecular dynamics simulation study（アデノシンA2a受容体とGタンパク質との結合のダイナミクスの解明：分子動力学シミュレーション研究による）2023
- Author(s)
  Duy Phuoc Tran, Sari Hagimoto and Akio Kitao
- Organizer
  第61回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-23K27138
[Presentation] Sampling the conformational transition of the monomer of Nsp15 of the SARS-nCoV2 gives a hint to inhibit its hexamer2023
- Author(s)
  Duy Phuoc Tran and Akio Kitao
- Organizer
  NanoBioCoM2023
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K27138
[Presentation] How the bacterial Flagellar Motor stator works: an insight from molecular dynamics simulation2023
- Author(s)
  Duy Phuoc Tran、Akio Kitao
- Organizer
  CCP2023
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K27138
[Presentation] How the mGLU1 receptor dimer be activated: a molecular dynamics study2023
- Author(s)
  Duy Phuoc Tran
- Organizer
  高速分子動画　国際シンポジウム2023
- Data Source
  KAKENHI-PROJECT-23K27138
[Presentation] How the bacterial Flagellar Motor stator works: an insight from molecular dynamics simulation2023
- Author(s)
  Duy Phuoc Tran, Akio Kitao
- Organizer
  The 34th IUPAP Conference on Computational Physiscs
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K14154
[Presentation] Unveiling the mGLU1 dimer dynamics during partially-active to inactive state transition2023
- Author(s)
  Duy Phuoc Tran、Kitao Akio
- Organizer
  令和５年度新学術領域研究「高速分子動画」シンポジウム
- Data Source
  KAKENHI-PROJECT-23K27138
[Presentation] When computer simulations meet machine learning: unveiling the dynamics of biomolecular complexes2020
- Author(s)
  Duy Tran, Akio Kitao
- Organizer
  The 9th Tokyo Tech International Symposium on Life Science and Technology
- Invited
- Data Source
  KAKENHI-PROJECT-19K23721
[Presentation] DNA binding mechanisms of the p53 C-terminal domain elucidated by MD simulation2020
- Author(s)
  Yuta Taira, Duy Tran, Akio Kitao
- Organizer
  The 58th Annual Meeting of the Biophysical Society of Japan
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K23721
[Presentation] Biomolecular Functional Design: an Introduction to Recent Advances2020
- Author(s)
  Duy Tran
- Organizer
  The 58th Annual Meeting of the Biophysical Society of Japan
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K23721
[Presentation] Kinetic rate evaluation for protein complexes by PaCS-MD/MSM2020
- Author(s)
  Yoshiki Miyazawa, Phuoc Duy Tran, Kazuhiro Takemura, Akio Kitao
- Organizer
  The 58th Annual Meeting of the Biophysical Society of Japan
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K23721
[Presentation] Calculation of binding free energy and kinetic rates with flexible protein docking2019
- Author(s)
  Tran Phuoc Duy, Akio Kitao
- Organizer
  Annual Meeting of the Biophysical Society of Japan
- Invited
- Data Source
  KAKENHI-PROJECT-19K23721

1. 北尾彰朗 (30252422)

# of Collaborated Projects: 1 results

# of Collaborated Products: 6 results

TRAN PHUOC DUY ＴＲＡＮ ＰＨＵＯＣ・ＤＵＹ

TRAN PHUOC・DUY チャン フ・ズイ

Research Projects

Research Products

Co-Researchers

Investigating molecular interactions of p53 regulated by post translation modifications and intrinsically disordered regions with advanced simulation

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Ion permeation and rotation mechanisms in bacterial flagellar motor statorsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Atomistic mechanism of the oligomerization of p53 protein in DNA scanningPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Journal Article] PaCS-Toolkit: Optimized Software Utilities for Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Simulations and Subsequent Analyses2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Delineating the conformational landscape of the adenosine A2A receptor during G protein coupling2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Generating Ampicillin-Level Antimicrobial Peptides with Activity-Aware Generative Adversarial Networks2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] PaCS-MD/MSM : Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method2020

Author(s)

Journal Title

Data Source

[Journal Article] Kinetic Selection and Relaxation of the Intrinsically Disordered Region of a Protein upon Binding2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins2020

Author(s)

Journal Title

DOI

Data Source

[Presentation] べん毛モーター固定子MotA/Bタンパク質複合体のイオン透過シミュレーション(Simulating ion permeation through the flagellar motor stator MotA/B protein complexes)2024

Author(s)

Organizer

Data Source

[Presentation] Simulating ion permeation through the flagellar motor stator MotA/B protein complexes2024

Author(s)

Organizer

Data Source

[Presentation] Unveiling the dynamics of Adenosine A2a receptor coupling to the G proteins: a molecular dynamics simulation study（アデノシンA2a受容体とGタンパク質との結合のダイナミクスの解明： 分子動力学シミュレーション研究による）2023

Author(s)

Organizer

Data Source

[Presentation] Sampling the conformational transition of the monomer of Nsp15 of the SARS-nCoV2 gives a hint to inhibit its hexamer2023

Author(s)

Organizer

Data Source

[Presentation] How the bacterial Flagellar Motor stator works: an insight from molecular dynamics simulation2023

Author(s)

Organizer

Data Source

[Presentation] How the mGLU1 receptor dimer be activated: a molecular dynamics study2023

Author(s)

Organizer

Data Source

[Presentation] How the bacterial Flagellar Motor stator works: an insight from molecular dynamics simulation2023

Author(s)

Organizer

Data Source

TRAN PHUOC DUY ＴＲＡＮＰＨＵＯＣ・ＤＵＹ

TRAN PHUOC・DUY チャンフ・ズイ

[Presentation] Unveiling the dynamics of Adenosine A2a receptor coupling to the G proteins: a molecular dynamics simulation study（アデノシンA2a受容体とGタンパク質との結合のダイナミクスの解明：分子動力学シミュレーション研究による）2023