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Journal Abstract Search

388 related items for PubMed ID: 17113307

  • 1. 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; 157(3):514-23. PubMed ID: 17113307
    [Abstract] [Full Text] [Related]

  • 2. 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]

  • 3. 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 18; 157(3):524-33. PubMed ID: 17293125
    [Abstract] [Full Text] [Related]

  • 4. Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent.
    Kannan S, Zacharias M.
    Proteins; 2010 Oct 18; 78(13):2809-19. PubMed ID: 20635348
    [Abstract] [Full Text] [Related]

  • 5. 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]

  • 6. 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]

  • 7. 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]

  • 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. 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]

  • 10. How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach.
    Nymeyer H.
    J Chem Theory Comput; 2008 Apr 15; 4(4):626-36. PubMed ID: 26620937
    [Abstract] [Full Text] [Related]

  • 11. ETNA: equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations.
    Muff S, Caflisch A.
    J Phys Chem B; 2009 Mar 12; 113(10):3218-26. PubMed ID: 19231819
    [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 12; 43(3):172-80. PubMed ID: 21289072
    [Abstract] [Full Text] [Related]

  • 13. 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]

  • 14. Error and efficiency of replica exchange molecular dynamics simulations.
    Rosta E, Hummer G.
    J Chem Phys; 2009 Oct 28; 131(16):165102. PubMed ID: 19894977
    [Abstract] [Full Text] [Related]

  • 15. 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]

  • 16. Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models.
    Paschek D, Day R, García AE.
    Phys Chem Chem Phys; 2011 Nov 28; 13(44):19840-7. PubMed ID: 21845272
    [Abstract] [Full Text] [Related]

  • 17. 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]

  • 18. 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]

  • 19. Peptide folding kinetics from replica exchange molecular dynamics.
    Buchete NV, Hummer G.
    Phys Rev E Stat Nonlin Soft Matter Phys; 2008 Mar 17; 77(3 Pt 1):030902. PubMed ID: 18517321
    [Abstract] [Full Text] [Related]

  • 20. 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]

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