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堀 直人

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テキサス大学オースティン校 化学科
Thirumalaiグループ 博士研究員

研究内容

論文

  1. Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA
    Chakraborty D ; Hori N ; Thirumalai D
    J. Chem. Theory Comput. (2018) 14(7): 3763-3779 10.1021/acs.jctc.8b00091    [bioRxiv] [arXiv]
  2. Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot
    Roca J ; Hori N ; Baral S ; Velmurugu Y ; Narayanan R ; Narayanan P ; Thirumalai D ; Ansari A
    Proc. Natl. Acad. Sci. U. S. A. (2018) in press 10.1073/pnas.1717582115    [bioRxiv] [arXiv]
  3. Protein Collapse is Encoded in the Folded State Architecture.
    Samanta HS ; Zhuravlev PI ; Hinczewski M ; Hori N ; Chakrabarti S ; Thirumalai D
    Soft Matter (2017) 13(19): 3622-3638 10.1039/C7SM00074J    [arXiv]
  4. Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension
    Hori N ; Denesyuk NA ; Thirumalai D
    J. Mol. Biol. (2016) 428(14): 2847-2859 10.1016/j.jmb.2016.06.002    [arXiv]
  5. How co-translational folding of multi-domain protein is affected by elongation schedule: Molecular simulations
    Tanaka T ; Hori N ; Takada S
    PLoS Comput. Biol. (2015) 11(7): e1004356 10.1371/journal.pcbi.1004356    [PDF]
  6. Coarse-grained structure-based model for RNA-protein complexes developed by fluctuation matching
    Hori N ; Takada S
    J. Chem. Theory Comput. (2012) 8(9): 3384-3394 10.1021/ct300361j
  7. CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work
    Kenzaki H ; Koga N ; Hori N ; Kanada R ; Li W ; Okazaki K ; Yao XQ ; Takada S
    J. Chem. Theory Comput. (2011) 7(6): 1979-1989 10.1021/ct2001045
  8. Multiscale methods for protein folding simulations
    Li W ; Yoshii H ; Hori N ; Kameda T ; Takada S
    Methods (2010) 52: 106-114 10.1016/j.ymeth.2010.04.014
  9. Folding energy landscape and network dynamics of small globular proteins
    Hori N ; Chikenji G ; Berry RS ; Takada S
    Proc. Natl. Acad. Sci. U. S. A. (2009) 106: 73-78 10.1073/pnas.0811560106     [PDF]

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