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 *

140 related articles for article (PubMed ID: 25580188)

  • 1. Differential Impact of the Monovalent Ions Li⁺, Na⁺, K⁺, and Rb⁺ on DNA Conformational Properties.
    Savelyev A; MacKerell AD
    J Phys Chem Lett; 2015 Jan; 6(1):212-6. PubMed ID: 25580188
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding.
    Savelyev A; MacKerell AD
    J Chem Theory Comput; 2015 Sep; 11(9):4473-85. PubMed ID: 26575937
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields.
    Savelyev A; MacKerell AD
    J Phys Chem B; 2015 Mar; 119(12):4428-40. PubMed ID: 25751286
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Polarizable Molecular Dynamics Simulations of Two
    Salsbury AM; Dean TJ; Lemkul JA
    J Chem Theory Comput; 2020 May; 16(5):3430-3444. PubMed ID: 32307997
    [TBL] [Abstract][Full Text] [Related]  

  • 5. The effects of monovalent cations Li+, Na+, K+, NH4+, Rb+ and Cs+ on the solid and solution structures of the nucleic acid components. Metal ion binding and sugar conformation.
    Tajmir-Riahi HA; Messaoudi S
    J Biomol Struct Dyn; 1992 Oct; 10(2):345-65. PubMed ID: 1334674
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field.
    Prajapati JD; Mele C; Aksoyoglu MA; Winterhalter M; Kleinekathöfer U
    J Chem Inf Model; 2020 Jun; 60(6):3188-3203. PubMed ID: 32479082
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Monovalent cation size and DNA conformational stability.
    Stellwagen E; Muse JM; Stellwagen NC
    Biochemistry; 2011 Apr; 50(15):3084-94. PubMed ID: 21410141
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA.
    Lemkul JA; MacKerell AD
    J Chem Theory Comput; 2017 May; 13(5):2072-2085. PubMed ID: 28398748
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.
    Savelyev A; MacKerell AD
    J Phys Chem B; 2014 Jun; 118(24):6742-57. PubMed ID: 24874104
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Monovalent cation binding in the minor groove of DNA A-tracts.
    Dong Q; Stellwagen E; Stellwagen NC
    Biochemistry; 2009 Feb; 48(5):1047-55. PubMed ID: 19154116
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Prediction of the concentration dependence of the surface tension and density of salt solutions: atomistic simulations using Drude oscillator polarizable and nonpolarizable models.
    Neyt JC; Wender A; Lachet V; Ghoufi A; Malfreyt P
    Phys Chem Chem Phys; 2013 Jul; 15(28):11679-90. PubMed ID: 23752676
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.
    Yu H; Whitfield TW; Harder E; Lamoureux G; Vorobyov I; Anisimov VM; Mackerell AD; Roux B
    J Chem Theory Comput; 2010; 6(3):774-786. PubMed ID: 20300554
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Probing hydration of monovalent cations condensed around polymeric nucleic acids.
    Tikhomirova A; Chalikian TV
    J Mol Biol; 2004 Aug; 341(2):551-63. PubMed ID: 15276843
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Allosteric interactions between DNA strands and monovalent cations in DNA quadruplex assembly: thermodynamic evidence for three linked association pathways.
    Hardin CC; Corregan MJ; Lieberman DV; Brown BA
    Biochemistry; 1997 Dec; 36(49):15428-50. PubMed ID: 9398273
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations.
    Robbins TJ; Wang Y
    J Biomol Struct Dyn; 2013; 31(11):1311-23. PubMed ID: 23153112
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Counterion distribution surrounding spherical nucleic acid-Au nanoparticle conjugates probed by small-angle x-ray scattering.
    Kewalramani S; Zwanikken JW; Macfarlane RJ; Leung CY; Olvera de la Cruz M; Mirkin CA; Bedzyk MJ
    ACS Nano; 2013 Dec; 7(12):11301-9. PubMed ID: 24251367
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field.
    Li H; Ngo V; Da Silva MC; Salahub DR; Callahan K; Roux B; Noskov SY
    J Phys Chem B; 2015 Jul; 119(29):9401-16. PubMed ID: 25578354
    [TBL] [Abstract][Full Text] [Related]  

  • 18. All-atom polarizable force field for DNA based on the classical Drude oscillator model.
    Savelyev A; MacKerell AD
    J Comput Chem; 2014 Jun; 35(16):1219-39. PubMed ID: 24752978
    [TBL] [Abstract][Full Text] [Related]  

  • 19. The impact of monovalent ion force field model in nucleic acids simulations.
    Noy A; Soteras I; Luque FJ; Orozco M
    Phys Chem Chem Phys; 2009 Dec; 11(45):10596-607. PubMed ID: 20145804
    [TBL] [Abstract][Full Text] [Related]  

  • 20. DNA and its counterions: a molecular dynamics study.
    Várnai P; Zakrzewska K
    Nucleic Acids Res; 2004; 32(14):4269-80. PubMed ID: 15304564
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.