"Duy Phuoc Tran,Kitao Akio","Unveiling the mGLU1 dimer dynamics during partially-active to inactive state transition","高速分子動画 国際シンポジウム2023",,,,,,2024,Nov.
"Duy Phuoc Tran,Sari Hagimoto,Akio Kitao","Unveiling the dynamics of Adenosine A2a receptor coupling to the G proteins: a molecular dynamics simulation study","Annual Meeting of Biophysical Society of Japan",,,,,,2023,Nov.
"Duy Phuoc Tran,Akio Kitao","Revealing the functional roles of the complex formation/deformation of tumor suppressor p53 protein","The Tenth Project Report Meeting of the HPCI System Including Fugaku",,,,,,2023,Oct.
"Duy Phuoc Tran,Akio Kitao","Sampling the conformational transition of the monomer of Nsp15 of the SARS-nCoV2 gives a hint to inhibit its hexamer","NanoBioCoM2023",,,,,,2023,Sept.
"Duy Phuoc Tran,Akio Kitao","How the bacterial Flagellar Motor stator works: an insight from molecular dynamics simulation",,,,,,,2023,Aug.
"Mariko Kojima,Satoshi Abe,Tadaomi Furuta,Duy Phuoc Tran,Kunio Hirata,Keitaro Yamashita,Yuki Hishikawa,Akio Kitao,Takafumi Ueno","Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein",,"Biomater. Sci.",,"vol. 11","no. 4","pp. 1350-1357",2023,Feb.
"Duy Phuoc Tran,Akio Kitao","Revealing the complex formation/deformation process of antitumor suppressor p53 protein complexes in functioning","10TH ASIA-PACIFIC ASSOCIATION OF THEORETICAL AND COMPUTATIONAL CHEMISTRY CONFERENCE (APATCC)",,,,,,2023,Feb.
"中矢光,TranPhuoc Duy,北尾彰朗","並列カスケード選択分子動力学法を用いた生体分子の解離過程解析","第16回分子科学討論会",,,,,,2022,Sept.
"Mariko Kojima,Yuki Hishikawa,Satoshi Abe,Tadaomi Furuta,Duy Phuoc Tran,Akio Kitao,Takafumi Ueno","Dynamics structural analysis of miniprotein by in-cell crystal engineering","The 102nd CSJ Annual Meeting (2022)",,,,,,2022,Mar.
"Duy Phuoc Tran,Yuta Taira,Takumi Ogawa,Ryoga Misu,Yoshiki Miyazawa,Akio Kitao","Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer",,"Scientific Reports",,,,,2022,Mar.
"Hiroaki Hata,Duy Phuoc Tran,Marzouk,Akio Kitao","Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model",,"Biophysics and Physicobiology",,,,,2021,Dec.
"Duy Phuoc Tran,Akio Kitao","Calculation of Binding Free Energy and Kinetic Rates with Flexible Protein Docking",,"Seibutsu Butsuri",,"Vol. 61","No. 6","pp. 398-399",2021,Nov.
"Duy Tran,Akio Kitao","DNA bending enhances the dissociation of tetrameric p53’s coredomains","59th Annual Meeting of Biophysical Society of Japan",,,,,,2021,Nov.
"Duy Phuoc Tran,Akio Kitao","Binding free energy calculation with dPaCS-MD/MSM","C2C Program Kick off symposium",,,,,,2021,Oct.
"Duy Phuoc Tran,Akio Kitao","Atomic mechanism of the complete association of intrinsically disordered peptide to protein","XXXII IUPAP Conference on Computational Physics(CCP2021)",,,,,,2021,Aug.
"Duy Tran,Akio Kitao","Predicting the complex conformations of protein/intrinsically disordered peptide complexes","The Protein Society-35th Anniversary Symposium",,,,,,2021,July
"宮澤 佳希,Tran Phuoc Duy,竹村 和浩,北尾 彰朗","Parallel Cascade Selection Molecular Dynamics/Markov State Model によるタンパク質?タンパク質複合体の結合親和性評価 (Evaluation of binding affinity for protein-protein complexes by Parallel Cascade Selection Molecular Dynamics/Markov State Model","第21回日本蛋白質科学会年会",,,,,,2021,June
"チャン フ ズイ,畑 宏明,中矢 光,北尾彰朗","Benchmarking the free energy calculation of PaCS-MD/MSM","第21回日本蛋白質科学会年会",,,,,,2021,June
"Duy Phuoc Tran,Akio Kitao","Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides",,"Scientific Reports",,"Vol. 11","No. 1",,2021,May
"Mariko Kojima,Yuki Hishikawa,Satoshi Abe,Tadaomi Furuta,Duy Phuoc Tran,Akio Kitao,Takafumi Ueno","Energy Analysis of Miniprotein by in Vivo Protein Crystallization","日本化学会第101春季年会",,,,,,2021,Mar.
"平悠太,TranPhuoc Duy,北尾彰朗","分子動力学計算によるp53-C 末端部位のDNA 結合機構の解明","第34回分子シミュレーション討論会",,,,,,2020,Dec.
"宮澤佳希,TranPhuoc Duy,竹村和浩,北尾彰朗","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","第34回分子シミュレーション討論会",,,,,,2020,Dec.
"尾川拓巳,TranPhuoc Duy,藤井 高志,難波 啓一,北尾彰朗","PaCS-MDによるアクトミオシンの結合解離予測","第34回分子シミュレーション討論会 オンライン学会",,,,,,2020,Dec.
"平悠太,TranPhuoc Duy,北尾彰朗","分子動力学計算によるp53-C 末端部位のDNA 結合機構の解明",,,,,,,2020,Sept.
"宮澤佳希,TranPhuoc Duy,竹村和浩,北尾彰朗","PaCS-MD/MSM を用いたタンパク質複合体の速度定数評価",,,,,,,2020,Sept.
"Duy Phuoc Tran","Generating Ampicillin-Level Antimicrobial Peptides with Activity-Aware Generative Adversarial Networks",,"ACS Omega",,"Vol. 0","No. 0","pp. null",2020,Aug.
"Duy Phuoc Tran,Akio Kitao","Simulating the association/dissociation process of flexible protein complexes","第20回日本蛋白質科学会年会",,,,,,2020,July
"Yoshiki Miyazawa,Duy Phuoc Tran,Kazuhiro Takemura,Akio Kitao","Protein-protein complex dissociation simulated by Parallel Cascade Selection Molecular Dynamics","第20回日本蛋白質科学会年会",,,,,,2020,July
"Duy Phuoc Tran","Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins",,"The Journal of Chemical Physics",,,,,2020,June
"Duy Phuoc Tran,Hiroaki Hata,Takumi Ogawa,Yuta Taira,Akio Kitao","PaCS-MD/MSM: Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method",,"分子シミュレーション学会誌アンサンブル",,"Vol. 22",," 151-156",2020,Apr.
"Duy Phuoc Tran","Kinetic Selection and Relaxation of the Intrinsically Disordered Region of a Protein upon Binding",,"Journal of Chemical Theory and Computation",,,,,2020,Mar.
"Duy Phuoc Tran","Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method",,"ACS Omega",,,,,2019,Aug.
"Duy Phuoc Tran,Akio Kitao","Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model",,"The Journal of Physical Chemistry B",," 123"," 11"," 2469-2478",2019,Mar.
"Duy Phuoc Tran","Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model",,"The Journal of Physical Chemistry B",,,,,2019,Mar.
"Satoshi Yamashita,Misao Mizuno,Duy Phuoc Tran,Hisham Dokainish,Akio Kitao,Yasuhisa Mizutani","Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins",,"The Journal of Physical Chemistry B",,"Vol. 122","No. 22","pp. 5877-5884",2018,June
"Tran, D.P.,Lam, V.T.,Tran, T.L.,Nguyen, T.N.S.,Thi Tran, H.T.,Duy Phuoc Tran","In silico study of Bombyx mori fibroin enhancement by graphene in acidic environment",,"Physical Chemistry Chemical Physics",,"Vol. 20","No. 28","pp. 19240-19249",2018,
"Yamashita, S.,Mizuno, M.,Tran, D.P.,Dokainish, H.,Kitao, A.,Mizutani, Y.,Duy Phuoc Tran","Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins",,"Journal of Physical Chemistry B",,"Vol. 122","No. 22","pp. 5877-5884",2018,
"Tran, D.P.,Takemura, K.,Kuwata, K.,Kitao, A.,Duy Phuoc Tran","Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics",,"Journal of Chemical Theory and Computation",,"Vol. 14","No. 1","pp. 404-417",2018,
"Tran, D.P.,Lam, V.T.,Tran, T.L.,Nguyen, T.N.S.,Thi Tran, H.T.,Duy Phuoc Tran","In silico study of Bombyx mori fibroin enhancement by graphene in acidic environment",,"Physical Chemistry Chemical Physics",,"Vol. 20","No. 28","pp. 19240-19249",2018,
"Duy Phuoc Tran","Obtaining Binding Free Energy from a Path Sampling without Force Bias",,"Biophysical Journal",,,,,2016,Feb.
"Duy Phuoc Tran","Obtaining Binding Free Energy from a Path Sampling without Force Bias",,"Biophysical Journal",,,,,2016,Feb.
"Nguyen, T.T.,Tran, D.P.,Pham Dinh Quoc Huy,Hoang, Z.,Carloni, P.,Van Pham, P.,Nguyen, C.,Li, M.S.,Duy Phuoc Tran","Ligand binding to anti-cancer target CD44 investigated by molecular simulations",,"Journal of Molecular Modeling",,"Vol. 22","No. 7",,2016,
"Kitao, A.,Harada, R.,Nishihara, Y.,Tran, D.P.,Duy Phuoc Tran","Parallel cascade selection molecular dynamics for efficient conformational sampling and free energy calculation of proteins",,"AIP Conference Proceedings",,"Vol. 1790",,,2016,
"Nguyen, T.T.,Tran, D.P.,Pham Dinh Quoc Huy,Hoang, Z.,Carloni, P.,Van Pham, P.,Nguyen, C.,Li, M.S.,Duy Phuoc Tran","Ligand binding to anti-cancer target CD44 investigated by molecular simulations",,"Journal of Molecular Modeling",,"Vol. 22","No. 7",,2016,
"Kitao, A.,Harada, R.,Nishihara, Y.,Tran, D.P.,Duy Phuoc Tran","Parallel cascade selection molecular dynamics for efficient conformational sampling and free energy calculation of proteins",,"AIP Conference Proceedings",,"Vol. 1790",,,2016,
"Van Hoang, V.,Duy, T.P.,Duy Phuoc Tran","Melting of mesoscale lennard-jones crystals with free surfaces",,"Journal of the Physical Society of Japan",,"Vol. 82","No. 6",,2013,
"Van Hoang, V.,Duy, T.P.,Duy Phuoc Tran","Melting of mesoscale lennard-jones crystals with free surfaces",,"Journal of the Physical Society of Japan",,"Vol. 82","No. 6",,2013,
"Sandal, M.,Duy, T.P.,Cona, M.,Zung, H.,Carloni, P.,Musiani, F.,Giorgetti, A.,Duy Phuoc Tran","GOMoDo: A GPCRs Online Modeling and Docking Webserver",,"PLoS ONE",,"Vol. 8","No. 9",,2013,
"Sandal, M.,Duy, T.P.,Cona, M.,Zung, H.,Carloni, P.,Musiani, F.,Giorgetti, A.,Duy Phuoc Tran","GOMoDo: A GPCRs Online Modeling and Docking Webserver",,"PLoS ONE",,"Vol. 8","No. 9",,2013,
"Phuoc Duy, T.,Van Hoang, V.,Duy Phuoc Tran","Atomic mechanism of homogeneous melting of bcc Fe at the limit of superheating",,"Physica B: Condensed Matter",,"Vol. 407","No. 6","pp. 978-984",2012,
"Hanh, T.T.T.,Hoang, V.V.,Duy, T.P.,Duy Phuoc Tran","Structural properties of simulated liquid GanAsm",,"Computational Materials Science",,"Vol. 54","No. 1","pp. 183-187",2012,
"Phuoc Duy, T.,Van Hoang, V.,Duy Phuoc Tran","Atomic mechanism of homogeneous melting of bcc Fe at the limit of superheating",,"Physica B: Condensed Matter",,"Vol. 407","No. 6","pp. 978-984",2012,
"Hanh, T.T.T.,Hoang, V.V.,Duy, T.P.,Duy Phuoc Tran","Structural properties of simulated liquid GanAsm",,"Computational Materials Science",,"Vol. 54","No. 1","pp. 183-187",2012,
"Hoang, V.V.,Duy, T.P.,Duy Phuoc Tran","Structural defects and thermodynamics of vitreous GeO2 nanoparticles",,"Current Applied Physics",,"Vol. 11","No. 3","pp. 303-310",2011,
"Hoang, V.V.,Duy, T.P.,Duy Phuoc Tran","Structural defects and thermodynamics of vitreous GeO2 nanoparticles",,"Current Applied Physics",,"Vol. 11","No. 3","pp. 303-310",2011,