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Journal Abstract Search

201 related items for PubMed ID: 21322666

  • 1. 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]

  • 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. 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]

  • 4. Replica exchange simulation method using temperature and solvent viscosity.
    Nguyen PH.
    J Chem Phys; 2010 Apr 14; 132(14):144109. PubMed ID: 20405987
    [Abstract] [Full Text] [Related]

  • 5. Rapid free energy calculation of peptide self-assembly by REMD umbrella sampling.
    Wolf MG, Jongejan JA, Laman JD, de Leeuw SW.
    J Phys Chem B; 2008 Oct 30; 112(43):13493-8. PubMed ID: 18841883
    [Abstract] [Full Text] [Related]

  • 6. Structure and energy landscape of a photoswitchable peptide: a replica exchange molecular dynamics study.
    Nguyen PH, Mu Y, Stock G.
    Proteins; 2005 Aug 15; 60(3):485-94. PubMed ID: 15977160
    [Abstract] [Full Text] [Related]

  • 7. An improved replica-exchange sampling method: temperature intervals with global energy reassignment.
    Li X, O'Brien CP, Collier G, Vellore NA, Wang F, Latour RA, Bruce DA, Stuart SJ.
    J Chem Phys; 2007 Oct 28; 127(16):164116. PubMed ID: 17979328
    [Abstract] [Full Text] [Related]

  • 8. 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]

  • 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. Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent.
    Kannan S, Zacharias M.
    Proteins; 2010 Oct 08; 78(13):2809-19. PubMed ID: 20635348
    [Abstract] [Full Text] [Related]

  • 11. Replica exchange molecular dynamics simulations of amyloid peptide aggregation.
    Cecchini M, Rao F, Seeber M, Caflisch A.
    J Chem Phys; 2004 Dec 01; 121(21):10748-56. PubMed ID: 15549960
    [Abstract] [Full Text] [Related]

  • 12. Structural and thermodynamics characters of isolated α-syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution.
    Cao Z, Liu L, Wu P, Wang J.
    Acta Biochim Biophys Sin (Shanghai); 2011 Mar 01; 43(3):172-80. PubMed ID: 21289072
    [Abstract] [Full Text] [Related]

  • 13. 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]

  • 14. Conformational space search of Neuromedin C using replica exchange molecular dynamics and molecular dynamics.
    Sharma P, Singh P, Bisetty K, Rodriguez A, Perez JJ.
    J Pept Sci; 2011 Mar 18; 17(3):174-83. PubMed ID: 20878681
    [Abstract] [Full Text] [Related]

  • 15. Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space.
    Chen C, Xiao Y, Huang Y.
    Phys Rev E Stat Nonlin Soft Matter Phys; 2015 May 18; 91(5):052708. PubMed ID: 26066200
    [Abstract] [Full Text] [Related]

  • 16. Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles.
    Ostermeir K, Zacharias M.
    J Comput Chem; 2014 Jan 15; 35(2):150-8. PubMed ID: 24318649
    [Abstract] [Full Text] [Related]

  • 17. A hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper.
    Cukier RI.
    J Chem Phys; 2011 Jan 28; 134(4):045104. PubMed ID: 21280805
    [Abstract] [Full Text] [Related]

  • 18. 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]

  • 19. Does Replica Exchange with Solute Tempering Efficiently Sample Aβ Peptide Conformational Ensembles?
    Smith AK, Lockhart C, Klimov DK.
    J Chem Theory Comput; 2016 Oct 11; 12(10):5201-5214. PubMed ID: 27560127
    [Abstract] [Full Text] [Related]

  • 20. 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]

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