| Delineating the conformational landscape of the adenosine A2A receptor during G protein coupling SK Huang, A Pandey, DP Tran, NL Villanueva, A Kitao, RK Sunahara, ... Cell 184 (7), 1884-1894. e14, 2021 | 107 | 2021 |
| GOMoDo: a GPCRs online modeling and docking webserver M Sandal, TP Duy, M Cona, H Zung, P Carloni, F Musiani, A Giorgetti PloS one 8 (9), e74092, 2013 | 84 | 2013 |
| Generating ampicillin-level antimicrobial peptides with activity-aware generative adversarial networks A Tucs, DP Tran, A Yumoto, Y Ito, T Uzawa, K Tsuda ACS Omega 5 (36), 22847, 2020 | 60 | 2020 |
| Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model DP Tran, A Kitao The Journal of Physical Chemistry B 123 (11), 2469-2478, 2019 | 48 | 2019 |
| Protein–ligand dissociation simulated by parallel cascade selection molecular dynamics DP Tran, K Takemura, K Kuwata, A Kitao Journal of chemical theory and computation 14 (1), 404-417, 2018 | 45 | 2018 |
| Vibrational energy transfer from heme through atomic contacts in proteins S Yamashita, M Mizuno, DP Tran, H Dokainish, A Kitao, Y Mizutani The Journal of Physical Chemistry B 122 (22), 5877-5884, 2018 | 38 | 2018 |
| Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method K Shin, DP Tran, K Takemura, A Kitao, K Terayama, K Tsuda ACS omega 4 (9), 13853-13862, 2019 | 28 | 2019 |
| Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model H Hata, DP Tran, MM Sobeh, A Kitao Biophysics and Physicobiology 18, 305-316, 2021 | 26 | 2021 |
| Parallel cascade selection molecular dynamics for efficient conformational sampling and free energy calculation of proteins A Kitao, R Harada, Y Nishihara, DP Tran AIP Conference Proceedings 1790 (1), 2016 | 25 | 2016 |
| Atomic mechanism of homogeneous melting of bcc Fe at the limit of superheating TP Duy, V Van Hoang Physica B: Condensed Matter 407 (6), 978-984, 2012 | 23 | 2012 |
| Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides DP Tran, S Tada, A Yumoto, A Kitao, Y Ito, T Uzawa, K Tsuda Scientific Reports 11 (1), 10630, 2021 | 21 | 2021 |
| Kinetic selection and relaxation of the Intrinsically Disordered Region of a Protein upon Binding DP Tran, A Kitao Journal of Chemical Theory and Computation 16 (4), 2835-2845, 2020 | 21 | 2020 |
| Ligand binding to anti-cancer target CD44 investigated by molecular simulations TT Nguyen, DP Tran, PDQ Huy, Z Hoang, P Carloni, P Van Pham, ... Journal of molecular modeling 22, 1-14, 2016 | 14 | 2016 |
| Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins K Takaba, DP Tran, A Kitao The Journal of Chemical Physics 152 (22), 2020 | 8 | 2020 |
| In silico study of Bombyx mori fibroin enhancement by graphene in acidic environment DP Tran, VT Lam, TL Tran, TNS Nguyen, HTT Tran Physical Chemistry Chemical Physics 20 (28), 19240-19249, 2018 | 7 | 2018 |
| Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer DP Tran, Y Taira, T Ogawa, R Misu, Y Miyazawa, A Kitao Scientific reports 12 (1), 3860, 2022 | 5 | 2022 |
| Structural defects and thermodynamics of vitreous GeO2 nanoparticles V Van Hoang, TP Duy Current Applied Physics 11 (3), 303-310, 2011 | 3 | 2011 |
| Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein M Kojima, S Abe, T Furuta, DP Tran, K Hirata, K Yamashita, Y Hishikawa, ... Biomaterials Science 11 (4), 1350-1357, 2023 | 2 | 2023 |
| Structure of MotA, a flagellar stator protein, from hyperthermophile T Nishikino, N Takekawa, DP Tran, J Kishikawa, M Hirose, S Onoe, ... Biochemical and Biophysical Research Communications 631, 78-85, 2022 | 2 | 2022 |
| Melting of Mesoscale Lennard-Jones Crystals with Free Surfaces V Van Hoang, T Phuoc Duy Journal of the Physical Society of Japan 82 (6), 064601, 2013 | 2 | 2013 |
