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 *

160 related articles for article (PubMed ID: 28319659)

  • 1. 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]  

  • 2. 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]  

  • 3. 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]  

  • 4. 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]  

  • 5. Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs.
    Yildirim I; Kennedy SD; Stern HA; Hart JM; Kierzek R; Turner DH
    J Chem Theory Comput; 2012 Jan; 8(1):172-181. PubMed ID: 22249447
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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]  

  • 7. Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field.
    Zgarbová M; Jurečka P; Banáš P; Havrila M; Šponer J; Otyepka M
    J Phys Chem B; 2017 Mar; 121(11):2420-2433. PubMed ID: 28290207
    [TBL] [Abstract][Full Text] [Related]  

  • 8. 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]  

  • 9. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes.
    Tucker MR; Piana S; Tan D; LeVine MV; Shaw DE
    J Phys Chem B; 2022 Jun; 126(24):4442-4457. PubMed ID: 35694853
    [TBL] [Abstract][Full Text] [Related]  

  • 10. 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]  

  • 11. 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]  

  • 12. Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.
    Aliev AE; Courtier-Murias D
    J Phys Chem B; 2010 Sep; 114(38):12358-75. PubMed ID: 20825228
    [TBL] [Abstract][Full Text] [Related]  

  • 13. 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]  

  • 14. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields.
    Havrila M; Zgarbová M; Jurečka P; Banáš P; Krepl M; Otyepka M; Šponer J
    J Phys Chem B; 2015 Dec; 119(49):15176-90. PubMed ID: 26548477
    [TBL] [Abstract][Full Text] [Related]  

  • 15. 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]  

  • 16. Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.
    Yildirim I; Stern HA; Kennedy SD; Tubbs JD; Turner DH
    J Chem Theory Comput; 2010 May; 6(5):1520-1531. PubMed ID: 20463845
    [TBL] [Abstract][Full Text] [Related]  

  • 17. AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.
    Zhang C; Lu C; Jing Z; Wu C; Piquemal JP; Ponder JW; Ren P
    J Chem Theory Comput; 2018 Apr; 14(4):2084-2108. PubMed ID: 29438622
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives.
    Dutta N; Deb I; Sarzynska J; Lahiri A
    J Comput Aided Mol Des; 2022 Mar; 36(3):205-224. PubMed ID: 35338419
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results.
    Langley DR
    J Biomol Struct Dyn; 1998 Dec; 16(3):487-509. PubMed ID: 10052609
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields.
    Fadrná E; Špačková N; Sarzyñska J; Koča J; Orozco M; Cheatham TE; Kulinski T; Šponer J
    J Chem Theory Comput; 2009 Sep; 5(9):2514-30. PubMed ID: 26616629
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.