Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein Reviewed International journal

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

Structure of MotA, a flagellar stator protein, from hyperthermophile Reviewed International journal

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

Biochemical and Biophysical Research Communications   631   78 - 85   2022.11

Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer Reviewed International journal

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

Scientific Reports   12 ( 1 )   3860 - 3860   2022.4

Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides Reviewed International journal

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

Scientific Reports   11 ( 1 )   10630 - 10630   2021.12

Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model Reviewed

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

Biophysics and Physicobiology   18   305 - 316   2021.12

Calculation of Binding Free Energy and Kinetic Rates with Flexible Protein Docking Invited Reviewed

Duy Phuoc TRAN, Akio KITAO

Seibutsu Butsuri   61 ( 6 )   398 - 399   2021.10

Delineating the conformational landscape of the adenosine A2A receptor during G protein coupling Reviewed International journal

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   2021.3

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) Reviewed International journal

Kenichiro Takaba, Duy Phuoc Tran, Akio Kitao

Journal of Chemical Physics   153 ( 17 )   179902 - 179902   2020.11

Generating Ampicillin-Level Antimicrobial Peptides with Activity-Aware Generative Adversarial Networks Reviewed International journal

Andrejs Tucs, Duy Phuoc Tran, Akiko Yumoto, Yoshihiro Ito, Takanori Uzawa, Koji Tsuda

ACS Omega   5 ( 36 )   22847 - 22851   2020.8

Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins Reviewed International journal

Kenichiro Takaba, Duy Phuoc Tran, Akio Kitao

The Journal of Chemical Physics   152 ( 22 )   225101 - 225101   2020.6

Kinetic Selection and Relaxation of the Intrinsically Disordered Region of a Protein upon Binding Reviewed International journal

Duy Phuoc Tran, Akio Kitao

Journal of Chemical Theory and Computation   16 ( 4 )   2835 - 2845   2020.4

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

Duy Phuoc Tran, Hiroaki Hata, Takumi Ogawa, Yuta Taira, Akio Kitao

Ensemble   22 ( 2 )   151 - 156   2020

Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method Reviewed International journal

Kento Shin, Duy Phuoc Tran, Kazuhiro Takemura, Akio Kitao, Kei Terayama, Koji Tsuda

ACS Omega   4 ( 9 )   13853 - 13862   2019.8

Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model Reviewed International journal

Duy Phuoc Tran, Kitao Akio

JOURNAL OF PHYSICAL CHEMISTRY B   123 ( 11 )   2469 - 2478   2019.3

In silico study of Bombyx mori fibroin enhancement by graphene in acidic environment Reviewed International journal

Duy Phuoc Tran, Vi Toan Lam, Tan Lien Tran, Thuy Nhu Son Nguyen, Hanh Thu Thi Tran

PHYSICAL CHEMISTRY CHEMICAL PHYSICS   20 ( 28 )   19240 - 19249   2018.7

Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins Reviewed International journal

Satoshi Yamashita, Misao Mizuno, Duy Phuoc Tran, Hisham Dokainish, Akio Kitao, Yasuhisa Mizutani

Journal of Physical Chemistry B   122 ( 22 )   5877 - 5884   2018.6

Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics Reviewed International journal

Duy Phuoc Tran, Kazuhiro Takemura, Kazuo Kuwata, Akio Kitao

Journal of Chemical Theory and Computation   14 ( 1 )   404 - 417   2018.1

Ligand binding to anti-cancer target CD44 investigated by molecular simulations Reviewed International journal

Tin Trung Nguyen, Duy Phuoc Tran, Pham Dinh Quoc Huy, Zung Hoang, Paolo Carloni, Phuc Van Pham, Chuong Nguyen, Mai Suan Li

JOURNAL OF MOLECULAR MODELING   22 ( 7 )   165 - 165   2016.7

Obtaining Binding Free Energy from a Path Sampling without Force Bias Reviewed

Duy Phuoc Tran, Akio Kitao

BIOPHYSICAL JOURNAL   110 ( 3 )   642A - 642A   2016.2

Parallel Cascade Selection Molecular Dynamics for Efficient Conformational Sampling and Free Energy Calculation of Proteins Reviewed

Akio Kitao, Ryuhei Harada, Yasutaka Nishihara, Duy Phuoc Tran

Proceedings of the International Conference of Computational Methods in Sciences and Engineering 2016 (ICCMSE-2016)   1790   2016

Melting of Mesoscale Lennard-Jones Crystals with Free Surfaces Reviewed

Vo Van Hoang, Tran Phuoc Duy

JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   82 ( 6 )   2013.6

GOMoDo: A GPCRs online modeling and docking webserver. Reviewed International journal

Massimo Sandal, Tran Phuoc Duy, Matteo Cona, Hoang Zung, Paolo Carloni, Francesco Musiani, Alejandro Giorgetti

PloS one   8 ( 9 )   e74092   2013

Structural properties of simulated liquid GanAsm Reviewed

Tran Thi Thu Hanh, Vo Van Hoang, Tran Phuoc Duy

COMPUTATIONAL MATERIALS SCIENCE   54 ( 1 )   183 - 187   2012.3

Atomic mechanism of homogeneous melting of bcc Fe at the limit of superheating Reviewed

Tran Phuoc Duy, Vo Van Hoang

PHYSICA B-CONDENSED MATTER   407 ( 6 )   978 - 984   2012.3

CHARACTERIZATION OF G PROTEIN COUPLED RECEPTORS THROUGH THE USE OF BIO-AND CHEMO-INFORMATICS TOOLS Reviewed

TP DUY, A GIORGETTI, NHAH CHUONG, P CARLONI, H ZUNG

Proc. Natl. Conf. Theor. Phys.   37   42 - 48   2012

Structural defects and thermodynamics of vitreous GeO2 nanoparticles Reviewed

Vo Van Hoang, Tran Phuoc Duy

CURRENT APPLIED PHYSICS   11 ( 3 )   303 - 310   2011.5

Parallel cascade selection molecular dynamics for analyzing dissociation process of biomolecules

中矢光, TRAN Phuoc duy, 北尾彰朗

分子科学討論会講演プログラム&要旨(Web)   16th   2022

Dynamics structural analysis of miniprotein by in-cell crystal engineering

KOJIMA Mariko, HISHIKAWA Yuki, ABE Satoshi, FURUTA Tadaomi, TRAN Duy Phuoc, KITAO Akio, UENO Takafumi

日本化学会春季年会講演予稿集(Web)   102nd   2022

How partial agonist ligands induce the conformational changes of Adenosine A2a receptor

TRAN Phuoc Duy, KITAO Akio

分子シミュレーション討論会講演要旨集   36th   2022

The relative motion of MotA around MotB in bacterial flagellar stator

TRAN Phuoc Duy, KITAO Akio

生物物理(Web)   62 ( Supplement 1-2 )   2022

Evaluation of binding affinity for protein-protein complexes by Parallel Cascade Selection Molecular Dynamics/Markov State Model

MIYAZAWA Yoshiki, PHUOC Tran Duy, TAKEMURA Kazuhiro, KITAO Akio

日本蛋白質科学会年会プログラム・要旨集   21st   2021

Calculation of Binding Free Energy and Kinetic Rates with Flexible Protein Docking

TRAN Duy Phuoc, KITAO Akio

生物物理(Web)   61 ( 6 )   2021

Benchmarking the free energy calculation of PaCS-MD/MSM

TRAN Phuoc Duy, HATA Hiroaki, NAKAYA Hikaru, KITAO Akio

日本蛋白質科学会年会プログラム・要旨集   21st   2021

Energy Analysis of Miniprotein by in Vivo Protein Crystallization

KOJIMA Mariko, HISHIKAWA Yuki, ABE Satoshi, FURUTA Tadaomi, TRAN Duy Phuoc, KITAO Akio, UENO Takafumi

日本化学会春季年会講演予稿集(Web)   101st   2021

Protein-protein complex dissociation simulated by Parallel Cascade Selection Molecular Dynamics

MIYAZAWA Yoshiki, TRAN Duy Phuoc, TAKEMURA Kazuhiro, KITAO Akio

日本蛋白質科学会年会プログラム・要旨集   20th (Web)   2020

PaCS-MD/MSMを用いたタンパク質-タンパク質複合体の結合親和性評価

宮澤佳希, DUY Tran Phuoc, 竹村和浩, 北尾彰朗

分子シミュレーション討論会講演要旨集   34th (CD-ROM)   2020

Biomolecular Functional Design: an Introduction to Recent Advances

TRAN Duy Phuoc

生物物理(Web)   60 ( Supplement 1-2 )   2020

Protein-protein complexes dissociation simulated by Parallel Cascade Selection Molecular Dynamics

MIYAZAWA Yoshiki, TRAN Duy Phuoc, TAKEMURA Kazuhiro, KITAO Akio

生物物理(Web)   59 ( Supplement 1-2 )   2019

Improvement of PaCS-MD based Flexible Docking Methods

TRAN Phuoc Duy, KITAO Akio

生物物理(Web)   57 ( Supplement 1-2 )   2017

Dimerization of CXCR4: a Steered Molecular Dynamics Study International conference

TRAN PHUOC DUY

the 1st International Workshop on Theoretical and Computational Physics  2013.7 

Characterization of G Protein Coupled Receptors through the Use of Bio- and Chemo- Informatics International conference

TRAN PHUOC DUY

the 37th National Conference on Theoretical Physics  2012.8 

Application of PaCS-MD to Free Energy Path Sampling International conference

TRAN PHUOC DUY

the 53th Annual Meeting of the Biophysical Society of Japan  2015.9 

Predicting Unbinding Pathway of Ligand through the Use of PaCS-MD International conference

TRAN PHUOC DUY

the 3rd Symposium on Studying the Function of Soft Molecular Systems by the Concerted Use of Theory and Experiment  2015.7 

Atomic Mechanism of Homogeneous Melting of bcc Fe at limit of Super-heating International conference

TRAN PHUOC DUY

the 35th National Conference on Theoretical Physics  2010.8 

Heterogeneous Melting of Nickel: New Insight from Atomic Mechanism International conference

TRAN PHUOC DUY

at the 37th National Conference on Theoretical Physics  2012.8 

Solidification of Vitreous Germania Nanoparticles International conference

TRAN PHUOC DUY

the 9th Asia Pacific Workshop on Materials Physics  2010.12 

Obtaining Binding Free Energy from Path Sampling without Force Bias International conference

TRAN PHUOC DUY

the Annual Meeting of Biophysical Society  2016.2 

Free Energy Path Sampling by PaCS-MD

TRAN PHUOC DUY

Science Camping of Soft Molecular Systems  2015.11 

Dissociation/Association Path Sampling without Biased Forces via PaCS-MD International conference

TRAN PHUOC DUY

the 16th Annual Meeting of the Protein Science Society of Japan  2016.6 

Improvement of PaCS-MD based Flexible Docking Method

TRAN PHUOC DUY

Science Camping on Studying the Function of Soft Molecular Systems by the Concerted Use of Theory and Experiment  2017.12 

Improvement of PaCS-MD based Flexible Docking Method International conference

TRAN PHUOC DUY

the 55th Annual Meeting of Biophysical Society of Japan  2017.9 

Application of machine learning methods in computational biophysics: from learning to reinforcement learning International conference

TRAN PHUOC DUY

International Conference on Computational Science and Engineering 4  2019.7 

In silico study of Bombyx mori fibroin enhancement by graphene in acidic environment International conference

TRAN PHUOC DUY

Computational Biophysics at the Molecular and Mesoscales  2018.10 

Flexible-Body Protein-Protein Docking: an Application of Parallel Cascade Selection MD International conference

TRAN PHUOC DUY

the 54th Annual Meeting of the Biophysical Society of Japan  2016.11 

Deactivating the Activated Human Adenosine A2A Receptor: a PaCS-MD Study

TRAN PHUOC DUY

the 4th Symposium on Studying the Function of Soft Molecular Systems by the Concerted Use of Theory and Experiment  2016.10 

Flexible Protein/Peptide Docking using PaCS-MD

TRAN PHUOC DUY

Symposium on Studying the Function of Soft Molecular Systems by the Concerted Use of Theory and Experiment  2017.6 

Association/Dissociation Path Sampling from the View of Selective Short Simulation Concatenation International conference

TRAN PHUOC DUY

the 3rd International Conference on Computational Science and Engineering  2016.11 

Biomolecular Functional Design: an Introduction to Recent Advances Invited

Tran Phuoc Duy

the Annual Meeting of the Biophysical Society of Japan  2020 

Calculation of binding free energy and kinetic rates with flexible protein docking International conference

TRAN PHUOC DUY, Akio Kitao

Annual Meeting of the Biophysical Society of Japan  2019.9 

When computer simulations meet machine learning: unveiling the dynamics of biomolecular complexes Invited

Duy Phuoc Tran, Akio Kitao

the 9th Tokyo Tech International Symposium on Life Science and Technology: Visualization and Engineering of Biomolecules  2021 

Revealing the functional roles of the complex formation/dissociation of tumor suppressor p53 protein

Duy Phuoc Tran, Akio Kitao

The Tenth Project Report Meeting of the HPCI System Including Fugaku  2023.10 

Sampling the conformational transition of the monomer of Nsp15 of the SARS-nCoV2 gives a hint to inhibit its hexamer

Duy Phuoc Tran, Akio Kitao

NanoBioCOM2023  2023.9 

How partial agonist ligands induce the conformational changes of Adenosine A2a receptor

Duy Tran, Masahiro Nara, Sari Hagimoto, Akio Kitao

2023.8 

How the bacterial Flagellar Motor stator works: an insight from molecular dynamics simulation

Duy Phuoc Tran, Akio Kitao

the 34th IUPAP Conference on Computational Physics  2023.8 

Ions Permeation through the Stators of Bacterial Flagellar Motors

Duy Phuoc Tran, Akio Kitao

NanoBioCoM2024  2024.3 

Simulating ion permeation through the flagellar motor stator MotA/B protein complexes

Duy Tran, Tatsuro Nishikino, Norihiro Takekawa, Seiji Kojima, Katsumi Imada, Michio Homma, Akio Kitao

Flagellar Meeting 2023  2024.3 

How the mGLU1 receptor dimer be activated: a molecular dynamics study

Duy Phuoc Tran, Yuya Fujihara, Akio Kitao

2023.12 

Decoupling processes of the Adenosine A2A receptor from G- proteins through the lens of dPaCS-MD simulations

Duy Tran, Louis-Philippe Picard, Alexander Orazietti, Sari Hagimoto, Adnan Sljoka, R. Scott Prosser, Akio Kitao

Annual Meeting of the Biophysical Society of Japan 2023  2023.11 

Unveiling the state transitions of the Adenosine A2A receptor using Molecular Dynamics Simulation

Duy Phuoc Tran, Akio Kitao

2023.5 

The relative motions of MotA and MotB in flagellar stator toward ion permeation

Flagellar Meeting  2023.3 

Revealing the complex formation/deformation process of antitumor suppressor p53 protein complexes in functioning

Tran Phuoc Duy, Kitao Akio

the 10th Asia Pacific Association on Theoretical and Computational Chemistry  2023.2 

Toward in silico precision drug design via the usage of massively parallelized path sampling algorithm PaCS-MD

Duy Phuoc Tran, Akio Kitao

Fugaku Exchange Meeting  2023.2 

How EGCG perturbs the interactions between MDM2 and N-terminal domain of p53

Duy Phuoc Tran, Akio Kitao

The 22nd Annual Meeting of the Protein Science Society of Japan  2022.6 

Benchmarking the free energy calculation of PaCS-MD/MSM

Duy Tran, Hiroaki Hata, Hikaru Nakaya, Akio Kitao

Annual meeting of the Protein Science Society of Japan  2021.6 

p53タンパク質のC末端ドメインとDNAの結合過程の解明

Non-domain biology Symposium 

Identification of sodium ion penetration pathways through the PomAB stator using SMD

Duy Tran, Tatsuro Nishikino, Norihiro Takekawa, Seiji Kojima, Katsumi Imada, Michio Homma, Akio Kitao

Flagellar meeting 2024  2025.3 

Signal Transduction in Class A GPCRs

Duy Phuoc Tran, Akio Kitao

The 2nd Area “Generative Design to Unlock the Potential of Protein Function” Meeting  2024.12 

Leveraging Biomolecular Simulations for Sustainable Development: from understanding to design

Duy Phuoc Tran, Akio Kitao

VANJ conference 2024  2024.12 

Signal Transduction in G-protein Coupled Receptors Class A and Class C Invited

Duy Phuoc Tran, Akio Kitao

THE 4TH KEYLAB INTERNATIONAL CONFERENCE EXPERIMENTAL AND COMPUTATIONAL APPROACHES IN MOLECULAR MEDICINE  2024.10 

In silico design of the activity-aware ligand coupled to the Adenosine A2A receptor

Duy Phuoc Tran, Akio Kitao

The 3rd Meeting of the Area "Protein Design" Symposium  2025.6 

Understanding the G protein activation pathway through the Adenosine A2A receptor using PaCS-MD/MSM

Duy Phuoc Tran, Akio Kitao

The 11th Asia Pacific Association of Theoretical and Computational Chemistry  2025.4 

Leveraging Biomolecular Simulations for Sustainable Development: from understanding to design

Duy Phuoc Tran

INTERNATIONAL CONFERENCE ON ENGINEERING AND TECHNOLOGIES FOR SUSTAINABLE DEVELOPMENT ICETSD 2024  2024.8 

Decoupling processes of the Adenosine A2A receptor from G- proteins through the lens of dPaCS-MD simulations

Duy Phuoc Tran, Akio Kitao

IUPAB 2024  2024.6 

Understanding the amino acid recognition by Medaka taste receptor T1R2a/T1R3

Duy Phuoc Tran, Vi Toan Lam, Atsuko Yamashita, Akio Kitao

KAKENHI Scientific Transformation (A) 'Material Symbiosis' area conference  2024.6 

Vallet Scholarship

2013   Rencontres du Vietnam  

TRAN PHUOC DUY

Praise of the Research Achievement in Academic Year 2011-2012

2013   Vietnam National University Hochiminh  

TRAN PHUOC DUY

Ion permeation and rotation mechanisms in bacterial flagellar motor stators

Grant number：hp230077  2023.4 - 2024.3

HPCI System Research Project  Fugaku Junior Researchers: FY2023 (Period A) 

How viral protein interfere the interactions of p53 protein with DNA

2022.4 - 2023.3

HPCI  FY 2022 HPCI General Access Category of the Supercomputer Fugaku - Junior Researchers Projects 

Atomistic mechanism of the oligomerization of p53 protein in DNA scanning

2019.8 - 2021.3

Ministry of Education, Culture, Sports, Science and Technology  Grant-in-Aid for Research Activity start-up 

TRAN PHUOC DUY

Association and dissociation simulations of bio-molecular complex using parallel cascade selection molecular dynamics

2014.10 - 2017.9

Hitachi Global Foundation  Hitachi Scholarship 

TRAN PHUOC DUY

Study of structural and phase transition in free surface and confined geometry system using computer simulation

2013.3 - 2015.3

Vietnam National Foundation for Science and Technology Development (Nafosted)  Natural Science Funding Program 

Vo Van Hoang, Tran Phuoc Duy

Molecular basis of odorant ligands recognition: a computational study

2012.3 - 2013.3

Vietnam National Foundation for Science and Technology Development (Nafosted)  Initiation and Enhancement of Bilateral Cooperation 

Hoang Zung, Nguyen Ha Hung Chuong, Tran Phuoc Duy, Nguyen Van Khoe

In silico study of structural and phase transition of the glassy nanoparticles

2009.9 - 2011.9

Vietnam National University Hochiminh  Foundation for Science and Technology 

Vo Van Hoang, Tran Phuoc Duy

In silico study of phase transition mechanism of monatomic system

Vietnam National University Hochiminh  Foundation for Science and Technology 

Vo Van Hoang, Tran Phuoc Duy