@article{CTT100885818,
  author = {Mariko Kojima and Satoshi Abe and Tadaomi Furuta and Duy Phuoc Tran and Kunio Hirata and Keitaro Yamashita and Yuki Hishikawa and Akio Kitao and Takafumi Ueno},
  title = {Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein},
  journal = {Biomater. Sci.},
  year = 2023,
}

@article{CTT100874612,
  author = {Duy Phuoc Tran and Yuta Taira and Takumi Ogawa and Ryoga Misu and Yoshiki Miyazawa and Akio Kitao},
  title = {Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer},
  journal = {Scientific Reports},
  year = 2022,
}

@article{CTT100874622,
  author = {Hiroaki Hata and Duy Phuoc Tran and Marzouk and Akio Kitao},
  title = {Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model},
  journal = {Biophysics and Physicobiology},
  year = 2021,
}

@article{CTT100851847,
  author = {Duy Phuoc Tran and Akio Kitao},
  title = {Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides},
  journal = {Scientific Reports},
  year = 2021,
}

@article{CTT100836623,
  author = {Duy Phuoc Tran},
  title = {Generating Ampicillin-Level Antimicrobial Peptides with Activity-Aware Generative Adversarial Networks},
  journal = {ACS Omega},
  year = 2020,
}

@article{CTT100836624,
  author = {Duy Phuoc Tran},
  title = {Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins},
  journal = {The Journal of Chemical Physics},
  year = 2020,
}

@article{CTT100837909,
  author = {Duy Phuoc Tran},
  title = {Kinetic Selection and Relaxation of the Intrinsically Disordered Region of a Protein upon Binding},
  journal = {Journal of Chemical Theory and Computation},
  year = 2020,
}

@article{CTT100836626,
  author = {Duy Phuoc Tran},
  title = {Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method},
  journal = {ACS Omega},
  year = 2019,
}

@article{CTT100836627,
  author = {Duy Phuoc Tran},
  title = {Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model},
  journal = {The Journal of Physical Chemistry B},
  year = 2019,
}

@article{CTT100809997,
  author = {Duy Phuoc Tran and Akio Kitao},
  title = {Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model},
  journal = {The Journal of Physical Chemistry B},
  year = 2019,
}

@article{CTT100809975,
  author = {Satoshi Yamashita and Misao Mizuno and Duy Phuoc Tran and Hisham Dokainish and Akio Kitao and Yasuhisa Mizutani},
  title = {Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins},
  journal = {The Journal of Physical Chemistry B},
  year = 2018,
}

@article{CTT100795011,
  author = {Tran, D.P. and Lam, V.T. and Tran, T.L. and Nguyen, T.N.S. and Thi Tran, H.T. and Duy Phuoc Tran},
  title = {In silico study of Bombyx mori fibroin enhancement by graphene in acidic environment},
  journal = {Physical Chemistry Chemical Physics},
  year = 2018,
}

@article{CTT100836628,
  author = {Tran, D.P. and Lam, V.T. and Tran, T.L. and Nguyen, T.N.S. and Thi Tran, H.T. and Duy Phuoc Tran},
  title = {In silico study of Bombyx mori fibroin enhancement by graphene in acidic environment},
  journal = {Physical Chemistry Chemical Physics},
  year = 2018,
}

@article{CTT100836629,
  author = {Tran, D.P. and Takemura, K. and Kuwata, K. and Kitao, A. and Duy Phuoc Tran},
  title = {Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics},
  journal = {Journal of Chemical Theory and Computation},
  year = 2018,
}

@article{CTT100836630,
  author = {Yamashita, S. and Mizuno, M. and Tran, D.P. and Dokainish, H. and Kitao, A. and Mizutani, Y. and Duy Phuoc Tran},
  title = {Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins},
  journal = {Journal of Physical Chemistry B},
  year = 2018,
}

@article{CTT100836631,
  author = {Duy Phuoc Tran},
  title = {Obtaining Binding Free Energy from a Path Sampling without Force Bias},
  journal = {Biophysical Journal},
  year = 2016,
}

@article{CTT100795014,
  author = {Duy Phuoc Tran},
  title = {Obtaining Binding Free Energy from a Path Sampling without Force Bias},
  journal = {Biophysical Journal},
  year = 2016,
}

@article{CTT100836632,
  author = {Nguyen, T.T. and Tran, D.P. and Pham Dinh Quoc Huy and Hoang, Z. and Carloni, P. and Van Pham, P. and Nguyen, C. and Li, M.S. and Duy Phuoc Tran},
  title = {Ligand binding to anti-cancer target CD44 investigated by molecular simulations},
  journal = {Journal of Molecular Modeling},
  year = 2016,
}

@article{CTT100795015,
  author = {Nguyen, T.T. and Tran, D.P. and Pham Dinh Quoc Huy and Hoang, Z. and Carloni, P. and Van Pham, P. and Nguyen, C. and Li, M.S. and Duy Phuoc Tran},
  title = {Ligand binding to anti-cancer target CD44 investigated by molecular simulations},
  journal = {Journal of Molecular Modeling},
  year = 2016,
}

@article{CTT100795017,
  author = {Sandal, M. and Duy, T.P. and Cona, M. and Zung, H. and Carloni, P. and Musiani, F. and Giorgetti, A. and Duy Phuoc Tran},
  title = {GOMoDo: A GPCRs Online Modeling and Docking Webserver},
  journal = {PLoS ONE},
  year = 2013,
}

@article{CTT100836635,
  author = {Van Hoang, V. and Duy, T.P. and Duy Phuoc Tran},
  title = {Melting of mesoscale lennard-jones crystals with free surfaces},
  journal = {Journal of the Physical Society of Japan},
  year = 2013,
}

@article{CTT100836634,
  author = {Sandal, M. and Duy, T.P. and Cona, M. and Zung, H. and Carloni, P. and Musiani, F. and Giorgetti, A. and Duy Phuoc Tran},
  title = {GOMoDo: A GPCRs Online Modeling and Docking Webserver},
  journal = {PLoS ONE},
  year = 2013,
}

@article{CTT100795018,
  author = {Van Hoang, V. and Duy, T.P. and Duy Phuoc Tran},
  title = {Melting of mesoscale lennard-jones crystals with free surfaces},
  journal = {Journal of the Physical Society of Japan},
  year = 2013,
}

@article{CTT100795019,
  author = {Phuoc Duy, T. and Van Hoang, V. and Duy Phuoc Tran},
  title = {Atomic mechanism of homogeneous melting of bcc Fe at the limit of superheating},
  journal = {Physica B: Condensed Matter},
  year = 2012,
}

@article{CTT100836636,
  author = {Phuoc Duy, T. and Van Hoang, V. and Duy Phuoc Tran},
  title = {Atomic mechanism of homogeneous melting of bcc Fe at the limit of superheating},
  journal = {Physica B: Condensed Matter},
  year = 2012,
}

@article{CTT100836637,
  author = {Hanh, T.T.T. and Hoang, V.V. and Duy, T.P. and Duy Phuoc Tran},
  title = {Structural properties of simulated liquid Ga<inf>n</inf>As<inf>m</inf>},
  journal = {Computational Materials Science},
  year = 2012,
}

@article{CTT100795020,
  author = {Hanh, T.T.T. and Hoang, V.V. and Duy, T.P. and Duy Phuoc Tran},
  title = {Structural properties of simulated liquid Ga<inf>n</inf>As<inf>m</inf>},
  journal = {Computational Materials Science},
  year = 2012,
}

@article{CTT100795021,
  author = {Hoang, V.V. and Duy, T.P. and Duy Phuoc Tran},
  title = {Structural defects and thermodynamics of vitreous GeO2 nanoparticles},
  journal = {Current Applied Physics},
  year = 2011,
}

@article{CTT100836638,
  author = {Hoang, V.V. and Duy, T.P. and Duy Phuoc Tran},
  title = {Structural defects and thermodynamics of vitreous GeO2 nanoparticles},
  journal = {Current Applied Physics},
  year = 2011,
}

@inproceedings{CTT100882134,
  author = {中矢光 and TranPhuoc Duy and 北尾彰朗},
  title = {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},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100867453,
  author = {Mariko Kojima and Yuki Hishikawa and Satoshi Abe and Tadaomi Furuta and Duy Phuoc Tran and Akio Kitao and Takafumi Ueno},
  title = {Dynamics structural analysis of  miniprotein by in-cell crystal engineering},
  booktitle = {},
  year = 2022,
}

@inproceedings{CTT100874811,
  author = {Duy Tran and Akio Kitao},
  title = {DNA bending enhances the dissociation of tetrameric p53’s coredomains},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100874820,
  author = {Duy Phuoc Tran and Akio Kitao},
  title = {Binding free energy calculation with dPaCS-MD/MSM},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100874807,
  author = {Duy Phuoc Tran and Akio Kitao},
  title = {Atomic mechanism of the complete association of intrinsically disordered peptide to protein},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100874819,
  author = {Duy Tran and Akio Kitao},
  title = {Predicting the complex conformations of protein/intrinsically disordered peptide complexes},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100874813,
  author = {宮澤 佳希 and Tran Phuoc Duy and 竹村 和浩 and 北尾 彰朗},
  title = {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},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100874818,
  author = {チャン フ ズイ and 畑 宏明 and 中矢 光 and 北尾彰朗},
  title = {Benchmarking the free energy calculation of PaCS-MD/MSM},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100847106,
  author = {Mariko Kojima and Yuki Hishikawa and Satoshi Abe and Tadaomi Furuta and Duy Phuoc Tran and Akio Kitao and Takafumi Ueno},
  title = {Energy Analysis of Miniprotein by in Vivo Protein Crystallization},
  booktitle = {},
  year = 2021,
}

@inproceedings{CTT100851895,
  author = {平悠太 and TranPhuoc Duy and 北尾彰朗},
  title = {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},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100851900,
  author = {宮澤佳希 and TranPhuoc Duy and 竹村和浩 and 北尾彰朗},
  title = {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},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100851904,
  author = {尾川拓巳 and TranPhuoc Duy and 藤井 高志 and 難波 啓一 and 北尾彰朗},
  title = {PaCS-MDによるアクトミオシンの結合解離予測},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100851892,
  author = {平悠太 and TranPhuoc Duy and 北尾彰朗},
  title = {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},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100851887,
  author = {宮澤佳希 and TranPhuoc Duy and 竹村和浩 and 北尾彰朗},
  title = {PaCS-MD/MSM を用いたタンパク質複合体の速度定数評価},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100851871,
  author = {Duy Phuoc Tran and Akio Kitao},
  title = {Simulating the association/dissociation process of flexible protein complexes},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100851880,
  author = {Yoshiki Miyazawa and Duy Phuoc Tran and Kazuhiro Takemura and Akio Kitao},
  title = {Protein-protein complex dissociation simulated by Parallel Cascade Selection Molecular Dynamics},
  booktitle = {},
  year = 2020,
}

@inproceedings{CTT100795016,
  author = {Kitao, A. and Harada, R. and Nishihara, Y. and Tran, D.P. and Duy Phuoc Tran},
  title = {Parallel cascade selection molecular dynamics for efficient conformational sampling and free energy calculation of proteins},
  booktitle = {AIP Conference Proceedings},
  year = 2016,
}

@inproceedings{CTT100836633,
  author = {Kitao, A. and Harada, R. and Nishihara, Y. and Tran, D.P. and Duy Phuoc Tran},
  title = {Parallel cascade selection molecular dynamics for efficient conformational sampling and free energy calculation of proteins},
  booktitle = {AIP Conference Proceedings},
  year = 2016,
}

@misc{CTT100875329,
  author = {Duy Phuoc Tran and Akio Kitao},
  title = {Calculation of Binding Free Energy and Kinetic Rates with Flexible Protein Docking},
  year = 2021,
}

@misc{CTT100851910,
  author = {Duy Phuoc Tran and Hiroaki Hata and Takumi Ogawa and Yuta Taira and Akio Kitao},
  title = {PaCS-MD/MSM: Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method},
  year = 2020,
}