Tran DP - Search Results

1

Delineating the conformational landscape of the adenosine A_2A receptor during G protein coupling.

Huang SK, Pandey A, Tran DP, Villanueva NL, Kitao A, Sunahara RK, Sljoka A, Prosser RS. Huang SK, et al. Among authors: tran dp. Cell. 2021 Apr 1;184(7):1884-1894.e14. doi: 10.1016/j.cell.2021.02.041. Epub 2021 Mar 19. Cell. 2021. PMID: 33743210 Free PMC article.

2

Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics.

Tran DP, Takemura K, Kuwata K, Kitao A. Tran DP, et al. J Chem Theory Comput. 2018 Jan 9;14(1):404-417. doi: 10.1021/acs.jctc.7b00504. Epub 2017 Dec 8. J Chem Theory Comput. 2018. PMID: 29182324 Free article.

3

Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins.

Yamashita S, Mizuno M, Tran DP, Dokainish H, Kitao A, Mizutani Y. Yamashita S, et al. Among authors: tran dp. J Phys Chem B. 2018 Jun 7;122(22):5877-5884. doi: 10.1021/acs.jpcb.8b03518. Epub 2018 May 23. J Phys Chem B. 2018. PMID: 29746131

4

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

Tran DP, Kitao A. Tran DP, et al. J Phys Chem B. 2019 Mar 21;123(11):2469-2478. doi: 10.1021/acs.jpcb.8b10309. Epub 2019 Jan 30. J Phys Chem B. 2019. PMID: 30645121

5

Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method.

Shin K, Tran DP, Takemura K, Kitao A, Terayama K, Tsuda K. Shin K, et al. Among authors: tran dp. ACS Omega. 2019 Aug 19;4(9):13853-13862. doi: 10.1021/acsomega.9b01480. eCollection 2019 Aug 27. ACS Omega. 2019. PMID: 31497702 Free PMC article.

6

Kinetic Selection and Relaxation of the Intrinsically Disordered Region of a Protein upon Binding.

Tran DP, Kitao A. Tran DP, et al. J Chem Theory Comput. 2020 Apr 14;16(4):2835-2845. doi: 10.1021/acs.jctc.9b01203. Epub 2020 Apr 1. J Chem Theory Comput. 2020. PMID: 32192337 Free article.

7

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

Takaba K, Tran DP, Kitao A. Takaba K, et al. Among authors: tran dp. J Chem Phys. 2020 Jun 14;152(22):225101. doi: 10.1063/5.0004654. J Chem Phys. 2020. PMID: 32534517

8

Erratum: "Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins" [J. Chem. Phys. 152, 225101 (2020)].

Takaba K, Tran DP, Kitao A. Takaba K, et al. Among authors: tran dp. J Chem Phys. 2020 Nov 7;153(17):179902. doi: 10.1063/5.0032465. J Chem Phys. 2020. PMID: 33167629 No abstract available.

9

Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides.

Tran DP, Tada S, Yumoto A, Kitao A, Ito Y, Uzawa T, Tsuda K. Tran DP, et al. Sci Rep. 2021 May 20;11(1):10630. doi: 10.1038/s41598-021-90245-z. Sci Rep. 2021. PMID: 34017051 Free PMC article.

10

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

Tran DP, Taira Y, Ogawa T, Misu R, Miyazawa Y, Kitao A. Tran DP, et al. Sci Rep. 2022 Mar 9;12(1):3860. doi: 10.1038/s41598-022-07792-2. Sci Rep. 2022. PMID: 35264667 Free PMC article.

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