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Journal Abstract Search

905 related items for PubMed ID: 20701388

  • 1. Structural dynamics of the box C/D RNA kink-turn and its complex with proteins: the role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations.
    Spacková N, Réblová K, Sponer J.
    J Phys Chem B; 2010 Aug 19; 114(32):10581-93. PubMed ID: 20701388
    [Abstract] [Full Text] [Related]

  • 2. A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis.
    Réblová K, Šponer JE, Špačková N, Beššeová I, Šponer J.
    J Phys Chem B; 2011 Dec 01; 115(47):13897-910. PubMed ID: 21999672
    [Abstract] [Full Text] [Related]

  • 3. Ribosomal RNA kink-turn motif--a flexible molecular hinge.
    Rázga F, Spackova N, Réblova K, Koca J, Leontis NB, Sponer J.
    J Biomol Struct Dyn; 2004 Oct 01; 22(2):183-94. PubMed ID: 15317479
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  • 5. Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding.
    Csaszar K, Spacková N, Stefl R, Sponer J, Leontis NB.
    J Mol Biol; 2001 Nov 09; 313(5):1073-91. PubMed ID: 11700064
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  • 6. Water and ion binding around RNA and DNA (C,G) oligomers.
    Auffinger P, Westhof E.
    J Mol Biol; 2000 Jul 28; 300(5):1113-31. PubMed ID: 10903858
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  • 7. Dependence of A-RNA simulations on the choice of the force field and salt strength.
    Besseová I, Otyepka M, Réblová K, Sponer J.
    Phys Chem Chem Phys; 2009 Dec 07; 11(45):10701-11. PubMed ID: 20145814
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  • 8. Water and ion binding around r(UpA)12 and d(TpA)12 oligomers--comparison with RNA and DNA (CpG)12 duplexes.
    Auffinger P, Westhof E.
    J Mol Biol; 2001 Feb 02; 305(5):1057-72. PubMed ID: 11162114
    [Abstract] [Full Text] [Related]

  • 9. Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 A resolution.
    Hamma T, Ferré-D'Amaré AR.
    Structure; 2004 May 02; 12(5):893-903. PubMed ID: 15130481
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  • 10. Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops.
    Krepl M, Réblová K, Koča J, Sponer J.
    J Phys Chem B; 2013 May 09; 117(18):5540-55. PubMed ID: 23534440
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  • 12. The crystal structure of the Methanocaldococcus jannaschii multifunctional L7Ae RNA-binding protein reveals an induced-fit interaction with the box C/D RNAs.
    Suryadi J, Tran EJ, Maxwell ES, Brown BA.
    Biochemistry; 2005 Jul 19; 44(28):9657-72. PubMed ID: 16008351
    [Abstract] [Full Text] [Related]

  • 13. Molecular dynamics simulations of sarcin-ricin rRNA motif.
    Spacková N, Sponer J.
    Nucleic Acids Res; 2006 Jul 19; 34(2):697-708. PubMed ID: 16456030
    [Abstract] [Full Text] [Related]

  • 14. Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces.
    Ma B, Nussinov R.
    J Mol Biol; 2000 Mar 03; 296(4):1091-104. PubMed ID: 10686106
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  • 15. RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics.
    Rázga F, Zacharias M, Réblová K, Koca J, Sponer J.
    Structure; 2006 May 03; 14(5):825-35. PubMed ID: 16698544
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  • 18. Structure and dynamics of the hydration shells of the Zn(2+) ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations.
    Cauët E, Bogatko S, Weare JH, Fulton JL, Schenter GK, Bylaska EJ.
    J Chem Phys; 2010 May 21; 132(19):194502. PubMed ID: 20499974
    [Abstract] [Full Text] [Related]

  • 19. Structure, dynamics and hydration of the nogalamycin-d(ATGCAT)2Complex determined by NMR and molecular dynamics simulations in solution.
    Williams HE, Searle MS.
    J Mol Biol; 1999 Jul 16; 290(3):699-716. PubMed ID: 10395824
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  • 20. Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop.
    Li W, Ma B, Shapiro B.
    J Biomol Struct Dyn; 2001 Dec 16; 19(3):381-96. PubMed ID: 11790138
    [Abstract] [Full Text] [Related]

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