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Journal Abstract Search


231 related items for PubMed ID: 12112673

  • 1. Assessing equilibration and convergence in biomolecular simulations.
    Smith LJ, Daura X, van Gunsteren WF.
    Proteins; 2002 Aug 15; 48(3):487-96. PubMed ID: 12112673
    [Abstract] [Full Text] [Related]

  • 2. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent.
    Periole X, Mark AE.
    J Chem Phys; 2007 Jan 07; 126(1):014903. PubMed ID: 17212515
    [Abstract] [Full Text] [Related]

  • 3. 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]

  • 4. Molecular dynamics simulations of peptide fragments from hen lysozyme: insight into non-native protein conformations.
    Smith LJ, Mark AE, Dobson CM, van Gunsteren WF.
    J Mol Biol; 1998 Jul 24; 280(4):703-19. PubMed ID: 9677298
    [Abstract] [Full Text] [Related]

  • 5. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
    Hassan SA, Mehler EL, Zhang D, Weinstein H.
    Proteins; 2003 Apr 01; 51(1):109-25. PubMed ID: 12596268
    [Abstract] [Full Text] [Related]

  • 6. On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: a molecular dynamics simulation study.
    Glättli A, Daura X, Bindschädler P, Jaun B, Mahajan YR, Mathad RI, Rueping M, Seebach D, van Gunsteren WF.
    Chemistry; 2005 Dec 09; 11(24):7276-93. PubMed ID: 16247825
    [Abstract] [Full Text] [Related]

  • 7. Conformational dynamics of cytochrome c: correlation to hydrogen exchange.
    García AE, Hummer G.
    Proteins; 1999 Aug 01; 36(2):175-91. PubMed ID: 10398365
    [Abstract] [Full Text] [Related]

  • 8. Convergence in peptide folding simulation: multiple trajectories of a potential AIDS pharmacophore.
    Mihailescu D, Reed J, Smith JC.
    Biopolymers; 2003 Oct 01; 70(2):121-33. PubMed ID: 14517902
    [Abstract] [Full Text] [Related]

  • 9. Numerical simulation of the effect of solvent viscosity on the motions of a beta-peptide heptamer.
    Gee PJ, van Gunsteren WF.
    Chemistry; 2005 Dec 16; 12(1):72-5. PubMed ID: 16259034
    [Abstract] [Full Text] [Related]

  • 10. Molecular dynamics simulation of folding of a short helical peptide with many charged residues.
    Wei CC, Ho MH, Wang WH, Sun YC.
    J Phys Chem B; 2005 Oct 27; 109(42):19980-6. PubMed ID: 16853583
    [Abstract] [Full Text] [Related]

  • 11. Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model.
    Smith AV, Hall CK.
    J Mol Biol; 2001 Sep 07; 312(1):187-202. PubMed ID: 11545596
    [Abstract] [Full Text] [Related]

  • 12. beta-hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution.
    Santiveri CM, Jiménez MA, Rico M, Van Gunsteren WF, Daura X.
    J Pept Sci; 2004 Sep 07; 10(9):546-65. PubMed ID: 15473263
    [Abstract] [Full Text] [Related]

  • 13. Simulation study on the disordered state of an Alzheimer's beta amyloid peptide Abeta(12 36) in water consisting of random-structural, beta-structural, and helical clusters.
    Ikebe J, Kamiya N, Ito J, Shindo H, Higo J.
    Protein Sci; 2007 Aug 07; 16(8):1596-608. PubMed ID: 17656579
    [Abstract] [Full Text] [Related]

  • 14. Comparative study of generalized born models: Born radii and peptide folding.
    Zhu J, Alexov E, Honig B.
    J Phys Chem B; 2005 Feb 24; 109(7):3008-22. PubMed ID: 16851315
    [Abstract] [Full Text] [Related]

  • 15. Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study.
    Graf J, Nguyen PH, Stock G, Schwalbe H.
    J Am Chem Soc; 2007 Feb 07; 129(5):1179-89. PubMed ID: 17263399
    [Abstract] [Full Text] [Related]

  • 16. Characterization of the conformational space of a triple-stranded beta-sheet forming peptide with molecular dynamics simulations.
    Soto P, Colombo G.
    Proteins; 2004 Dec 01; 57(4):734-46. PubMed ID: 15390268
    [Abstract] [Full Text] [Related]

  • 17. Influence of backbone fluorine substitution upon the folding equilibrium of a beta-heptapeptide.
    Gattin Z, van Gunsteren WF.
    J Phys Chem B; 2009 Jun 25; 113(25):8695-703. PubMed ID: 19485309
    [Abstract] [Full Text] [Related]

  • 18. 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]

  • 19. Establishing effective simulation protocols for beta- and alpha/beta-peptides. II. Molecular mechanical (MM) model for a cyclic beta-residue.
    Zhu X, Koenig P, Gellman SH, Yethiraj A, Cui Q.
    J Phys Chem B; 2008 May 01; 112(17):5439-48. PubMed ID: 18402479
    [Abstract] [Full Text] [Related]

  • 20. Convergence of replica exchange molecular dynamics.
    Zhang W, Wu C, Duan Y.
    J Chem Phys; 2005 Oct 15; 123(15):154105. PubMed ID: 16252940
    [Abstract] [Full Text] [Related]


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