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453 related items for PubMed ID: 15836251

  • 1. The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage.
    Linhananta A, Boer J, MacKay I.
    J Chem Phys; 2005 Mar 15; 122(11):114901. PubMed ID: 15836251
    [Abstract] [Full Text] [Related]

  • 2. Dynamics and cooperativity of Trp-cage folding.
    Hu Z, Tang Y, Wang H, Zhang X, Lei M.
    Arch Biochem Biophys; 2008 Jul 15; 475(2):140-7. PubMed ID: 18474213
    [Abstract] [Full Text] [Related]

  • 3. The folding pathway of ubiquitin from all-atom molecular dynamics simulations.
    Marianayagam NJ, Jackson SE.
    Biophys Chem; 2004 Oct 01; 111(2):159-71. PubMed ID: 15381313
    [Abstract] [Full Text] [Related]

  • 4. Free energy landscape of protein folding in water: explicit vs. implicit solvent.
    Zhou R.
    Proteins; 2003 Nov 01; 53(2):148-61. PubMed ID: 14517967
    [Abstract] [Full Text] [Related]

  • 5. Folding dynamics of the Trp-cage miniprotein: evidence for a native-like intermediate from combined time-resolved vibrational spectroscopy and molecular dynamics simulations.
    Meuzelaar H, Marino KA, Huerta-Viga A, Panman MR, Smeenk LE, Kettelarij AJ, van Maarseveen JH, Timmerman P, Bolhuis PG, Woutersen S.
    J Phys Chem B; 2013 Oct 03; 117(39):11490-501. PubMed ID: 24050152
    [Abstract] [Full Text] [Related]

  • 6. Ultrafast folding of a computationally designed Trp-cage mutant: Trp2-cage.
    Bunagan MR, Yang X, Saven JG, Gai F.
    J Phys Chem B; 2006 Mar 02; 110(8):3759-63. PubMed ID: 16494434
    [Abstract] [Full Text] [Related]

  • 7. Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations.
    Kannan S, Zacharias M.
    Proteins; 2009 Aug 01; 76(2):448-60. PubMed ID: 19173315
    [Abstract] [Full Text] [Related]

  • 8. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation.
    Shimada J, Kussell EL, Shakhnovich EI.
    J Mol Biol; 2001 Apr 20; 308(1):79-95. PubMed ID: 11302709
    [Abstract] [Full Text] [Related]

  • 9. Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide.
    Chowdhury S, Zhang W, Wu C, Xiong G, Duan Y.
    Biopolymers; 2003 Jan 20; 68(1):63-75. PubMed ID: 12579580
    [Abstract] [Full Text] [Related]

  • 10. Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.
    Paschek D, Nymeyer H, García AE.
    J Struct Biol; 2007 Mar 20; 157(3):524-33. PubMed ID: 17293125
    [Abstract] [Full Text] [Related]

  • 11. Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer.
    Nymeyer H, Woolf TB, Garcia AE.
    Proteins; 2005 Jun 01; 59(4):783-90. PubMed ID: 15828005
    [Abstract] [Full Text] [Related]

  • 12. Multiple folding mechanisms of protein ubiquitin.
    Zhang J, Qin M, Wang W.
    Proteins; 2005 May 15; 59(3):565-79. PubMed ID: 15768406
    [Abstract] [Full Text] [Related]

  • 13. Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model alpha-helical hairpin peptide.
    Chapagain PP, Gerstman BS.
    Biopolymers; 2006 Feb 15; 81(3):167-78. PubMed ID: 16215990
    [Abstract] [Full Text] [Related]

  • 14. Conformational equilibrium in alanine-rich peptides probed by reversible stretching simulations.
    Hénin J, Schulten K, Chipot C.
    J Phys Chem B; 2006 Aug 24; 110(33):16718-23. PubMed ID: 16913811
    [Abstract] [Full Text] [Related]

  • 15. Protonation/deprotonation effects on the stability of the Trp-cage miniprotein.
    Jimenez-Cruz CA, Makhatadze GI, Garcia AE.
    Phys Chem Chem Phys; 2011 Oct 14; 13(38):17056-63. PubMed ID: 21773639
    [Abstract] [Full Text] [Related]

  • 16. Explicit-chain model of native-state hydrogen exchange: implications for event ordering and cooperativity in protein folding.
    Kaya H, Chan HS.
    Proteins; 2005 Jan 01; 58(1):31-44. PubMed ID: 15468168
    [Abstract] [Full Text] [Related]

  • 17. Sampling the equilibrium kinetic network of Trp-cage in explicit solvent.
    Du W, Bolhuis PG.
    J Chem Phys; 2014 May 21; 140(19):195102. PubMed ID: 24852564
    [Abstract] [Full Text] [Related]

  • 18. Laser temperature jump study of the helix<==>coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model.
    Thompson PA, Eaton WA, Hofrichter J.
    Biochemistry; 1997 Jul 29; 36(30):9200-10. PubMed ID: 9230053
    [Abstract] [Full Text] [Related]

  • 19. Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models.
    Paschek D, Day R, García AE.
    Phys Chem Chem Phys; 2011 Nov 28; 13(44):19840-7. PubMed ID: 21845272
    [Abstract] [Full Text] [Related]

  • 20. Folding with downhill behavior and low cooperativity of proteins.
    Zuo G, Wang J, Wang W.
    Proteins; 2006 Apr 01; 63(1):165-73. PubMed ID: 16416404
    [Abstract] [Full Text] [Related]

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