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347 related items for PubMed ID: 18399522

  • 1. Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations.
    Boned R, van Gunsteren WF, Daura X.
    Chemistry; 2008; 14(16):5039-46. PubMed ID: 18399522
    [Abstract] [Full Text] [Related]

  • 2. Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.
    de Groot BL, Daura X, Mark AE, Grubmüller H.
    J Mol Biol; 2001 May 25; 309(1):299-313. PubMed ID: 11491298
    [Abstract] [Full Text] [Related]

  • 3. Structural, thermodynamic, and kinetic properties of Gramicidin analogue GS6 studied by molecular dynamics simulations and statistical mechanics.
    Zanetti-Polzi L, Anselmi M, D'Alessandro M, Amadei A, Di Nola A.
    Biopolymers; 2009 Dec 25; 91(12):1154-60. PubMed ID: 19396809
    [Abstract] [Full Text] [Related]

  • 4. Non-arrhenius behavior in the unfolding of a short, hydrophobic alpha-helix. Complementarity of molecular dynamics and lattice model simulations.
    Collet O, Chipot C.
    J Am Chem Soc; 2003 May 28; 125(21):6573-80. PubMed ID: 12785798
    [Abstract] [Full Text] [Related]

  • 5. Conformational energies and entropies of peptides, and the peptide-protein binding problem.
    Unal EB, Gursoy A, Erman B.
    Phys Biol; 2009 Jun 23; 6(3):036014. PubMed ID: 19549999
    [Abstract] [Full Text] [Related]

  • 6. Energy landscape of the trpzip2 peptide.
    Nymeyer H.
    J Phys Chem B; 2009 Jun 18; 113(24):8288-95. PubMed ID: 19469524
    [Abstract] [Full Text] [Related]

  • 7. For the sequence YKGQ, the turn and extended conformational forms are separated by small barriers and the turn propensity persists even at high temperatures: implications for protein folding.
    Kaur H, Sasidhar YU.
    J Phys Chem B; 2012 Mar 29; 116(12):3850-60. PubMed ID: 22385393
    [Abstract] [Full Text] [Related]

  • 8. Molecular dynamics simulations of a reversibly folding beta-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions.
    Reif MM, Kräutler V, Kastenholz MA, Daura X, Hünenberger PH.
    J Phys Chem B; 2009 Mar 12; 113(10):3112-28. PubMed ID: 19228001
    [Abstract] [Full Text] [Related]

  • 9. Evaluation of configurational entropy methods from peptide folding-unfolding simulation.
    Li DW, Khanlarzadeh M, Wang J, Huo S, Brüschweiler R.
    J Phys Chem B; 2007 Dec 13; 111(49):13807-13. PubMed ID: 18020439
    [Abstract] [Full Text] [Related]

  • 10. Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models.
    Yeh IC, Lee MS, Olson MA.
    J Phys Chem B; 2008 Nov 27; 112(47):15064-73. PubMed ID: 18959439
    [Abstract] [Full Text] [Related]

  • 11. Solvent electrostriction-driven peptide folding revealed by quasi-Gaussian entropy theory and molecular dynamics simulation.
    Noé F, Daidone I, Smith JC, di Nola A, Amadei A.
    J Phys Chem B; 2008 Sep 04; 112(35):11155-63. PubMed ID: 18698708
    [Abstract] [Full Text] [Related]

  • 12. New force replica exchange method and protein folding pathways probed by force-clamp technique.
    Kouza M, Hu CK, Li MS.
    J Chem Phys; 2008 Jan 28; 128(4):045103. PubMed ID: 18248010
    [Abstract] [Full Text] [Related]

  • 13. Simulated annealing coupled replica exchange molecular dynamics--an efficient conformational sampling method.
    Kannan S, Zacharias M.
    J Struct Biol; 2009 Jun 28; 166(3):288-94. PubMed ID: 19272454
    [Abstract] [Full Text] [Related]

  • 14. Reversible peptide folding in solution by molecular dynamics simulation.
    Daura X, Jaun B, Seebach D, van Gunsteren WF, Mark AE.
    J Mol Biol; 1998 Jul 31; 280(5):925-32. PubMed ID: 9671560
    [Abstract] [Full Text] [Related]

  • 15. The enthalpy change in protein folding and binding: refinement of parameters for structure-based calculations.
    Hilser VJ, Gómez J, Freire E.
    Proteins; 1996 Oct 31; 26(2):123-33. PubMed ID: 8916220
    [Abstract] [Full Text] [Related]

  • 16. Using one-step perturbation to predict the effect of changing force-field parameters on the simulated folding equilibrium of a beta-peptide in solution.
    Lin Z, Liu H, van Gunsteren WF.
    J Comput Chem; 2010 Oct 31; 31(13):2419-27. PubMed ID: 20652985
    [Abstract] [Full Text] [Related]

  • 17. Temperature dependence of three-body hydrophobic interactions: potential of mean force, enthalpy, entropy, heat capacity, and nonadditivity.
    Moghaddam MS, Shimizu S, Chan HS.
    J Am Chem Soc; 2005 Jan 12; 127(1):303-16. PubMed ID: 15631480
    [Abstract] [Full Text] [Related]

  • 18. Determination of the thermodynamics of carbonic anhydrase acid-unfolding by titration calorimetry.
    Baranauskiene L, Matuliene J, Matulis D.
    J Biochem Biophys Methods; 2008 Apr 24; 70(6):1043-7. PubMed ID: 18255160
    [Abstract] [Full Text] [Related]

  • 19. Enthalpy distribution for the alpha-helix/random coil transition in a model peptide: a study of two-state behavior.
    Poland D.
    Biopolymers; 2001 Apr 24; 60(4):317-21. PubMed ID: 11774234
    [Abstract] [Full Text] [Related]

  • 20. Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G.
    Zhou Y, Zhang C, Stell G, Wang J.
    J Am Chem Soc; 2003 May 21; 125(20):6300-5. PubMed ID: 12785863
    [Abstract] [Full Text] [Related]

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