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Journal Abstract Search

360 related items for PubMed ID: 20726603

  • 1. 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
    [Abstract] [Full Text] [Related]

  • 2. Dynamic ensemble view of the conformational landscape of HIV-1 TAR RNA and allosteric recognition.
    Lu J, Kadakkuzha BM, Zhao L, Fan M, Qi X, Xia T.
    Biochemistry; 2011 Jun 07; 50(22):5042-57. PubMed ID: 21553929
    [Abstract] [Full Text] [Related]

  • 3. The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein.
    Aboul-ela F, Karn J, Varani G.
    J Mol Biol; 1995 Oct 20; 253(2):313-32. PubMed ID: 7563092
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  • 4. Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics.
    Sarzyńska J, Réblová K, Sponer J, Kuliński T.
    Biopolymers; 2008 Sep 20; 89(9):732-46. PubMed ID: 18412127
    [Abstract] [Full Text] [Related]

  • 5. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.
    Al-Hashimi HM, Gosser Y, Gorin A, Hu W, Majumdar A, Patel DJ.
    J Mol Biol; 2002 Jan 11; 315(2):95-102. PubMed ID: 11779230
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  • 6. A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins.
    Ahmed A, Rippmann F, Barnickel G, Gohlke H.
    J Chem Inf Model; 2011 Jul 25; 51(7):1604-22. PubMed ID: 21639141
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  • 7. Role of conformational heterogeneity in ligand recognition by viral RNA molecules.
    Levintov L, Vashisth H.
    Phys Chem Chem Phys; 2021 May 19; 23(19):11211-11223. PubMed ID: 34010381
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  • 8. Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data.
    Schmitz U, Ulyanov NB, Kumar A, James TL.
    J Mol Biol; 1993 Nov 20; 234(2):373-89. PubMed ID: 8230221
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  • 9. Convergence of replica exchange molecular dynamics.
    Zhang W, Wu C, Duan Y.
    J Chem Phys; 2005 Oct 15; 123(15):154105. PubMed ID: 16252940
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  • 10. Dynamic ligand-induced-fit simulation via enhanced conformational samplings and ensemble dockings: a survivin example.
    Park IH, Li C.
    J Phys Chem B; 2010 Apr 22; 114(15):5144-53. PubMed ID: 20337446
    [Abstract] [Full Text] [Related]

  • 11. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking.
    Smith GR, Sternberg MJ, Bates PA.
    J Mol Biol; 2005 Apr 15; 347(5):1077-101. PubMed ID: 15784265
    [Abstract] [Full Text] [Related]

  • 12. 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 15; 17(3):174-83. PubMed ID: 20878681
    [Abstract] [Full Text] [Related]

  • 13. Characterization of the solution conformations of unbound and Tat peptide-bound forms of HIV-1 TAR RNA.
    Long KS, Crothers DM.
    Biochemistry; 1999 Aug 03; 38(31):10059-69. PubMed ID: 10433713
    [Abstract] [Full Text] [Related]

  • 14. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
    Hassan SA, Mehler EL, Zhang D, Weinstein H.
    Proteins; 2003 Apr 01; 51(1):109-25. PubMed ID: 12596268
    [Abstract] [Full Text] [Related]

  • 15. Conformational and dynamics changes induced by bile acids binding to chicken liver bile acid binding protein.
    Eberini I, Guerini Rocco A, Ientile AR, Baptista AM, Gianazza E, Tomaselli S, Molinari H, Ragona L.
    Proteins; 2008 Jun 01; 71(4):1889-98. PubMed ID: 18175325
    [Abstract] [Full Text] [Related]

  • 16. HiRE-RNA: a high resolution coarse-grained energy model for RNA.
    Pasquali S, Derreumaux P.
    J Phys Chem B; 2010 Sep 23; 114(37):11957-66. PubMed ID: 20795690
    [Abstract] [Full Text] [Related]

  • 17. RNA conformation in the Tat-TAR complex determined by site-specific photo-cross-linking.
    Wang Z, Rana TM.
    Biochemistry; 1996 May 21; 35(20):6491-9. PubMed ID: 8639596
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  • 18. Similarity of the 5' and 3'-TAR secondary structures in HIV-1.
    Wang P, Rouyez MC, Ducamp S, Saragosti S, Ventura M.
    Biochem Biophys Res Commun; 1993 Sep 15; 195(2):565-73. PubMed ID: 8373397
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  • 19. 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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  • 20. Visualizing spatially correlated dynamics that directs RNA conformational transitions.
    Zhang Q, Stelzer AC, Fisher CK, Al-Hashimi HM.
    Nature; 2007 Dec 20; 450(7173):1263-7. PubMed ID: 18097416
    [Abstract] [Full Text] [Related]

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