These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

217 related articles for article (PubMed ID: 23286901)

  • 1. The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics.
    Tubbs JD; Condon DE; Kennedy SD; Hauser M; Bevilacqua PC; Turner DH
    Biochemistry; 2013 Feb; 52(6):996-1010. PubMed ID: 23286901
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions.
    Yildirim I; Stern HA; Tubbs JD; Kennedy SD; Turner DH
    J Phys Chem B; 2011 Jul; 115(29):9261-70. PubMed ID: 21721539
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU).
    Condon DE; Yildirim I; Kennedy SD; Mort BC; Kierzek R; Turner DH
    J Phys Chem B; 2014 Feb; 118(5):1216-28. PubMed ID: 24377321
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Free energy profile of RNA hairpins: a molecular dynamics simulation study.
    Deng NJ; Cieplak P
    Biophys J; 2010 Feb; 98(4):627-36. PubMed ID: 20159159
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.
    Aytenfisu AH; Spasic A; Grossfield A; Stern HA; Mathews DH
    J Chem Theory Comput; 2017 Feb; 13(2):900-915. PubMed ID: 28048939
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Improving Computational Predictions of Single-Stranded RNA Tetramers with Revised α/γ Torsional Parameters for the Amber Force Field.
    Wales DJ; Yildirim I
    J Phys Chem B; 2017 Apr; 121(14):2989-2999. PubMed ID: 28319659
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Nuclear Magnetic Resonance Spectra and AMBER OL3 and ROC-RNA Simulations of UCUCGU Reveal Force Field Strengths and Weaknesses for Single-Stranded RNA.
    Zhao J; Kennedy SD; Turner DH
    J Chem Theory Comput; 2022 Feb; 18(2):1241-1254. PubMed ID: 34990548
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin.
    Giambaşu GM; York DM; Case DA
    RNA; 2015 May; 21(5):963-74. PubMed ID: 25805858
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field.
    Yildirim I
    Methods Mol Biol; 2019; 2022():55-74. PubMed ID: 31396899
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation.
    Spasic A; Kennedy SD; Needham L; Manoharan M; Kierzek R; Turner DH; Mathews DH
    RNA; 2018 May; 24(5):656-672. PubMed ID: 29434035
    [TBL] [Abstract][Full Text] [Related]  

  • 11. RNA force field with accuracy comparable to state-of-the-art protein force fields.
    Tan D; Piana S; Dirks RM; Shaw DE
    Proc Natl Acad Sci U S A; 2018 Feb; 115(7):E1346-E1355. PubMed ID: 29378935
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Interplay of LNA and 2'-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: a molecular dynamics study using the revised AMBER force field and comparison with experimental results.
    Yildirim I; Kierzek E; Kierzek R; Schatz GC
    J Phys Chem B; 2014 Dec; 118(49):14177-87. PubMed ID: 25268896
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Structural characterization of a six-nucleotide RNA hairpin loop found in Escherichia coli, r(UUAAGU).
    Zhang H; Fountain MA; Krugh TR
    Biochemistry; 2001 Aug; 40(33):9879-86. PubMed ID: 11502181
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Accuracy of MD solvent models in RNA structure refinement assessed via liquid-crystal NMR and spin relaxation data.
    Bergonzo C; Grishaev A
    J Struct Biol; 2019 Sep; 207(3):250-259. PubMed ID: 31279068
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Assessing the Current State of Amber Force Field Modifications for DNA.
    Galindo-Murillo R; Robertson JC; Zgarbová M; Šponer J; Otyepka M; Jurečka P; Cheatham TE
    J Chem Theory Comput; 2016 Aug; 12(8):4114-27. PubMed ID: 27300587
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Improved Force Field Parameters Lead to a Better Description of RNA Structure.
    Bergonzo C; Cheatham TE
    J Chem Theory Comput; 2015 Sep; 11(9):3969-72. PubMed ID: 26575892
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Empirical Corrections to the Amber RNA Force Field with Target Metadynamics.
    Gil-Ley A; Bottaro S; Bussi G
    J Chem Theory Comput; 2016 Jun; 12(6):2790-8. PubMed ID: 27153317
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Perturbation of DNA hairpins containing the EcoRI recognition site by hairpin loops of varying size and composition: physical (NMR and UV) and enzymatic (EcoRI) studies.
    Germann MW; Kalisch BW; Lundberg P; Vogel HJ; van de Sande JH
    Nucleic Acids Res; 1990 Mar; 18(6):1489-98. PubMed ID: 2326190
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops.
    Peritz AE; Kierzek R; Sugimoto N; Turner DH
    Biochemistry; 1991 Jul; 30(26):6428-36. PubMed ID: 1711369
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields.
    Bergonzo C; Henriksen NM; Roe DR; Cheatham TE
    RNA; 2015 Sep; 21(9):1578-90. PubMed ID: 26124199
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.