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166 related items for PubMed ID: 19399241

  • 1. Folding of Trp-cage mini protein using temperature and biasing potential replica-exchange molecular dynamics simulations.
    Kannan S, Zacharias M.
    Int J Mol Sci; 2009 Mar; 10(3):1121-37. PubMed ID: 19399241
    [Abstract] [Full Text] [Related]

  • 2. 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]

  • 3. 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]

  • 4. 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]

  • 5. Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.
    Zheng W, Gallicchio E, Deng N, Andrec M, Levy RM.
    J Phys Chem B; 2011 Feb 17; 115(6):1512-23. PubMed ID: 21254767
    [Abstract] [Full Text] [Related]

  • 6. Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach.
    Curuksu J, Zacharias M.
    J Chem Phys; 2009 Mar 14; 130(10):104110. PubMed ID: 19292526
    [Abstract] [Full Text] [Related]

  • 7. Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations.
    Kannan S, Zacharias M.
    PLoS One; 2014 Mar 14; 9(2):e88383. PubMed ID: 24563686
    [Abstract] [Full Text] [Related]

  • 8. Folding Thermodynamics and Mechanism of Five Trp-Cage Variants from Replica-Exchange MD Simulations with RSFF2 Force Field.
    Zhou CY, Jiang F, Wu YD.
    J Chem Theory Comput; 2015 Nov 10; 11(11):5473-80. PubMed ID: 26574335
    [Abstract] [Full Text] [Related]

  • 9. Folding dynamics of the Trp-cage miniprotein: evidence for a native-like intermediate from combined time-resolved vibrational spectroscopy and molecular dynamics simulations.
    Meuzelaar H, Marino KA, Huerta-Viga A, Panman MR, Smeenk LE, Kettelarij AJ, van Maarseveen JH, Timmerman P, Bolhuis PG, Woutersen S.
    J Phys Chem B; 2013 Oct 03; 117(39):11490-501. PubMed ID: 24050152
    [Abstract] [Full Text] [Related]

  • 10. Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations.
    Kamiya M, Sugita Y.
    J Chem Phys; 2018 Aug 21; 149(7):072304. PubMed ID: 30134668
    [Abstract] [Full Text] [Related]

  • 11. 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 21; 157(3):514-23. PubMed ID: 17113307
    [Abstract] [Full Text] [Related]

  • 12. Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.
    Paschek D, Nymeyer H, García AE.
    J Struct Biol; 2007 Mar 21; 157(3):524-33. PubMed ID: 17293125
    [Abstract] [Full Text] [Related]

  • 13. 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]

  • 14. Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations.
    Kannan S, Zacharias M.
    Biophys J; 2007 Nov 01; 93(9):3218-28. PubMed ID: 17660316
    [Abstract] [Full Text] [Related]

  • 15. Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein.
    Day R, Paschek D, Garcia AE.
    Proteins; 2010 Jun 01; 78(8):1889-99. PubMed ID: 20408169
    [Abstract] [Full Text] [Related]

  • 16. Trp-Cage Folding on Organic Surfaces.
    Levine ZA, Fischer SA, Shea JE, Pfaendtner J.
    J Phys Chem B; 2015 Aug 20; 119(33):10417-25. PubMed ID: 26207727
    [Abstract] [Full Text] [Related]

  • 17. Protonation/deprotonation effects on the stability of the Trp-cage miniprotein.
    Jimenez-Cruz CA, Makhatadze GI, Garcia AE.
    Phys Chem Chem Phys; 2011 Oct 14; 13(38):17056-63. PubMed ID: 21773639
    [Abstract] [Full Text] [Related]

  • 18. A comparative study of two different force fields on structural and thermodynamics character of H1 peptide via molecular dynamics simulations.
    Cao Z, Wang J.
    J Biomol Struct Dyn; 2010 Apr 14; 27(5):651-61. PubMed ID: 20085382
    [Abstract] [Full Text] [Related]

  • 19. Folding of small proteins using constrained molecular dynamics.
    Balaraman GS, Park IH, Jain A, Vaidehi N.
    J Phys Chem B; 2011 Jun 16; 115(23):7588-96. PubMed ID: 21591767
    [Abstract] [Full Text] [Related]

  • 20. How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory.
    Deng NJ, Dai W, Levy RM.
    J Phys Chem B; 2013 Oct 24; 117(42):12787-99. PubMed ID: 23705683
    [Abstract] [Full Text] [Related]

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