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152 related items for PubMed ID: 28964040

  • 1. Unraveling protein folding mechanism by analyzing the hierarchy of models with increasing level of detail.
    Hayashi T, Yasuda S, Škrbić T, Giacometti A, Kinoshita M.
    J Chem Phys; 2017 Sep 28; 147(12):125102. PubMed ID: 28964040
    [Abstract] [Full Text] [Related]

  • 2. Universal effects of solvent species on the stabilized structure of a protein.
    Hayashi T, Inoue M, Yasuda S, Petretto E, Škrbić T, Giacometti A, Kinoshita M.
    J Chem Phys; 2018 Jul 28; 149(4):045105. PubMed ID: 30068177
    [Abstract] [Full Text] [Related]

  • 3. Structural stability of proteins in aqueous and nonpolar environments.
    Yasuda S, Oshima H, Kinoshita M.
    J Chem Phys; 2012 Oct 07; 137(13):135103. PubMed ID: 23039615
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  • 4. Physical origins of the high structural stability of CLN025 with only ten residues.
    Yasuda S, Hayashi T, Kinoshita M.
    J Chem Phys; 2014 Sep 14; 141(10):105103. PubMed ID: 25217955
    [Abstract] [Full Text] [Related]

  • 5. Effects of side-chain packing on the formation of secondary structures in protein folding.
    Yasuda S, Yoshidome T, Oshima H, Kodama R, Harano Y, Kinoshita M.
    J Chem Phys; 2010 Feb 14; 132(6):065105. PubMed ID: 20151761
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  • 6. Entropy-Enthalpy Compensations Fold Proteins in Precise Ways.
    Li J, Hou C, Ma X, Guo S, Zhang H, Shi L, Liao C, Zheng B, Ye L, Yang L, He X.
    Int J Mol Sci; 2021 Sep 06; 22(17):. PubMed ID: 34502559
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  • 7. Analyses based on statistical thermodynamics for large difference between thermophilic rhodopsin and xanthorhodopsin in terms of thermostability.
    Yasuda S, Hayashi T, Kajiwara Y, Murata T, Kinoshita M.
    J Chem Phys; 2019 Feb 07; 150(5):055101. PubMed ID: 30736678
    [Abstract] [Full Text] [Related]

  • 8. Free-energy function based on an all-atom model for proteins.
    Yoshidome T, Oda K, Harano Y, Roth R, Sugita Y, Ikeguchi M, Kinoshita M.
    Proteins; 2009 Dec 07; 77(4):950-61. PubMed ID: 19688821
    [Abstract] [Full Text] [Related]

  • 9. Statistical and molecular dynamics studies of buried waters in globular proteins.
    Park S, Saven JG.
    Proteins; 2005 Aug 15; 60(3):450-63. PubMed ID: 15937899
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  • 10. Molecular dynamics simulations of folding processes of a beta-hairpin in an implicit solvent.
    Chen C, Xiao Y.
    Phys Biol; 2006 Aug 24; 3(3):161-71. PubMed ID: 17021380
    [Abstract] [Full Text] [Related]

  • 11. Free-energy function for discriminating the native fold of a protein from misfolded decoys.
    Yasuda S, Yoshidome T, Harano Y, Roth R, Oshima H, Oda K, Sugita Y, Ikeguchi M, Kinoshita M.
    Proteins; 2011 Jul 24; 79(7):2161-71. PubMed ID: 21557318
    [Abstract] [Full Text] [Related]

  • 12. Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: comparison between hard-sphere solvent and water.
    Oshima H, Kinoshita M.
    J Chem Phys; 2015 Apr 14; 142(14):145103. PubMed ID: 25877596
    [Abstract] [Full Text] [Related]

  • 13. On the Role of Entropy in the Stabilization of α-Helices.
    Bastida A, Zúñiga J, Requena A, Miguel B, Cerezo J.
    J Chem Inf Model; 2020 Dec 28; 60(12):6523-6531. PubMed ID: 33280379
    [Abstract] [Full Text] [Related]

  • 14. The occurrence of C--H...O hydrogen bonds in alpha-helices and helix termini in globular proteins.
    Manikandan K, Ramakumar S.
    Proteins; 2004 Sep 01; 56(4):768-81. PubMed ID: 15281129
    [Abstract] [Full Text] [Related]

  • 15. Stability of a model beta-sheet in water.
    Tobias DJ, Sneddon SF, Brooks CL.
    J Mol Biol; 1992 Oct 20; 227(4):1244-52. PubMed ID: 1433296
    [Abstract] [Full Text] [Related]

  • 16. Translational-entropy gain of solvent upon protein folding.
    Harano Y, Kinoshita M.
    Biophys J; 2005 Oct 20; 89(4):2701-10. PubMed ID: 16055541
    [Abstract] [Full Text] [Related]

  • 17. Crucial importance of translational entropy of water in pressure denaturation of proteins.
    Harano Y, Kinoshita M.
    J Chem Phys; 2006 Jul 14; 125(2):24910. PubMed ID: 16848614
    [Abstract] [Full Text] [Related]

  • 18. Entropy reduction effect imposed by hydrogen bond formation on protein folding cooperativity: evidence from a hydrophobic minimalist model.
    Barbosa MA, Garcia LG, Pereira de Araújo AF.
    Phys Rev E Stat Nonlin Soft Matter Phys; 2005 Nov 14; 72(5 Pt 1):051903. PubMed ID: 16383641
    [Abstract] [Full Text] [Related]

  • 19. Reframing the Protein Folding Problem: Entropy as Organizer.
    Rose GD.
    Biochemistry; 2021 Dec 14; 60(49):3753-3761. PubMed ID: 34855369
    [Abstract] [Full Text] [Related]

  • 20. Peptide folding driven by Van der Waals interactions.
    Sung SS.
    Protein Sci; 2015 Sep 14; 24(9):1383-8. PubMed ID: 26013298
    [Abstract] [Full Text] [Related]

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