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403 related items for PubMed ID: 15099840

  • 1.
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  • 3. Replica exchange molecular dynamics method for protein folding simulation.
    Zhou R.
    Methods Mol Biol; 2007; 350():205-23. PubMed ID: 16957325
    [Abstract] [Full Text] [Related]

  • 4. Free energy landscape and folding mechanism of a beta-hairpin in explicit water: a replica exchange molecular dynamics study.
    Nguyen PH, Stock G, Mittag E, Hu CK, Li MS.
    Proteins; 2005 Dec 01; 61(4):795-808. PubMed ID: 16240446
    [Abstract] [Full Text] [Related]

  • 5. Simulated annealing coupled replica exchange molecular dynamics--an efficient conformational sampling method.
    Kannan S, Zacharias M.
    J Struct Biol; 2009 Jun 01; 166(3):288-94. PubMed ID: 19272454
    [Abstract] [Full Text] [Related]

  • 6. Overcoming entropic barrier with coupled sampling at dual resolutions.
    Lwin TZ, Luo R.
    J Chem Phys; 2005 Nov 15; 123(19):194904. PubMed ID: 16321110
    [Abstract] [Full Text] [Related]

  • 7. Trp-cage: folding free energy landscape in explicit water.
    Zhou R.
    Proc Natl Acad Sci U S A; 2003 Nov 11; 100(23):13280-5. PubMed ID: 14581616
    [Abstract] [Full Text] [Related]

  • 8. 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]

  • 9. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.
    Chebaro Y, Dong X, Laghaei R, Derreumaux P, Mousseau N.
    J Phys Chem B; 2009 Jan 08; 113(1):267-74. PubMed ID: 19067549
    [Abstract] [Full Text] [Related]

  • 10. 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
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  • 11. A bias-exchange approach to protein folding.
    Piana S, Laio A.
    J Phys Chem B; 2007 May 03; 111(17):4553-9. PubMed ID: 17419610
    [Abstract] [Full Text] [Related]

  • 12. Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model.
    Felts AK, Harano Y, Gallicchio E, Levy RM.
    Proteins; 2004 Aug 01; 56(2):310-21. PubMed ID: 15211514
    [Abstract] [Full Text] [Related]

  • 13. The influence of different treatments of electrostatic interactions on the thermodynamics of folding of peptides.
    Baumketner A, Shea JE.
    J Phys Chem B; 2005 Nov 17; 109(45):21322-8. PubMed ID: 16853765
    [Abstract] [Full Text] [Related]

  • 14. Probing the free energy landscape of the FBP28WW domain using multiple techniques.
    Periole X, Allen LR, Tamiola K, Mark AE, Paci E.
    J Comput Chem; 2009 May 17; 30(7):1059-68. PubMed ID: 18942730
    [Abstract] [Full Text] [Related]

  • 15. Cooperative folding mechanism of a beta-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation.
    Yoda T, Sugita Y, Okamoto Y.
    Proteins; 2007 Mar 01; 66(4):846-59. PubMed ID: 17173285
    [Abstract] [Full Text] [Related]

  • 16. Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.
    Seibert MM, Patriksson A, Hess B, van der Spoel D.
    J Mol Biol; 2005 Nov 18; 354(1):173-83. PubMed ID: 16236315
    [Abstract] [Full Text] [Related]

  • 17. Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange.
    Mu Y.
    J Chem Phys; 2009 Apr 28; 130(16):164107. PubMed ID: 19405561
    [Abstract] [Full Text] [Related]

  • 18. An optimized replica exchange molecular dynamics method.
    Kamberaj H, van der Vaart A.
    J Chem Phys; 2009 Feb 21; 130(7):074906. PubMed ID: 19239315
    [Abstract] [Full Text] [Related]

  • 19. Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations.
    Ulmschneider JP, Ulmschneider MB, Di Nola A.
    J Phys Chem B; 2006 Aug 24; 110(33):16733-42. PubMed ID: 16913813
    [Abstract] [Full Text] [Related]

  • 20. 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]

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