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Journal Abstract Search

544 related items for PubMed ID: 16252940

  • 21. Reordering hydrogen bonds using hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems.
    Vreede J, Wolf MG, de Leeuw SW, Bolhuis PG.
    J Phys Chem B; 2009 May 07; 113(18):6484-94. PubMed ID: 19358572
    [Abstract] [Full Text] [Related]

  • 22. Optimization of replica exchange molecular dynamics by fast mimicking.
    Hritz J, Oostenbrink C.
    J Chem Phys; 2007 Nov 28; 127(20):204104. PubMed ID: 18052416
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  • 23. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential.
    Kannan S, Zacharias M.
    Proteins; 2007 Feb 15; 66(3):697-706. PubMed ID: 17120231
    [Abstract] [Full Text] [Related]

  • 24. Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations.
    Okamoto Y.
    J Mol Graph Model; 2004 May 15; 22(5):425-39. PubMed ID: 15099838
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  • 25. 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]

  • 26. Direct folding simulation of alpha-helices and beta-hairpins based on a single all-atom force field with an implicit solvation model.
    Jang S, Kim E, Pak Y.
    Proteins; 2007 Jan 01; 66(1):53-60. PubMed ID: 17063490
    [Abstract] [Full Text] [Related]

  • 27. 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]

  • 28. Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations.
    Beck DA, White GW, Daggett V.
    J Struct Biol; 2007 Mar 27; 157(3):514-23. PubMed ID: 17113307
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  • 29. 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 27; 10(9):546-65. PubMed ID: 15473263
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  • 30. 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
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  • 31. Multidimensional generalized-ensemble algorithms for complex systems.
    Mitsutake A, Okamoto Y.
    J Chem Phys; 2009 Jun 07; 130(21):214105. PubMed ID: 19508054
    [Abstract] [Full Text] [Related]

  • 32. Two-dimensional replica exchange approach for peptide-peptide interactions.
    Gee J, Shell MS.
    J Chem Phys; 2011 Feb 14; 134(6):064112. PubMed ID: 21322666
    [Abstract] [Full Text] [Related]

  • 33. Membrane adsorption, folding, insertion and translocation of synthetic trans-membrane peptides.
    Ulmschneider MB, Ulmschneider JP.
    Mol Membr Biol; 2008 Apr 14; 25(3):245-57. PubMed ID: 18428040
    [Abstract] [Full Text] [Related]

  • 34. 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
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  • 35. HIV-1 TAR RNA spontaneously undergoes relevant apo-to-holo conformational transitions in molecular dynamics and constrained geometrical simulations.
    Fulle S, Christ NA, Kestner E, Gohlke H.
    J Chem Inf Model; 2010 Aug 23; 50(8):1489-501. PubMed ID: 20726603
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  • 36. Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane.
    Ulmschneider JP, Ulmschneider MB, Di Nola A.
    Proteins; 2007 Nov 01; 69(2):297-308. PubMed ID: 17600830
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  • 37. Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm.
    Zhou R.
    J Mol Graph Model; 2004 May 01; 22(5):451-63. PubMed ID: 15099840
    [Abstract] [Full Text] [Related]

  • 38. Conformational sampling using high-temperature molecular dynamics.
    Bruccoleri RE, Karplus M.
    Biopolymers; 1990 Dec 01; 29(14):1847-62. PubMed ID: 2207289
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  • 39. 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
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  • 40. 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
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