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 *

128 related articles for article (PubMed ID: 33434436)

  • 1. Assessment of AMBER Force Fields for Simulations of ssDNA.
    Oweida TJ; Kim HS; Donald JM; Singh A; Yingling YG
    J Chem Theory Comput; 2021 Feb; 17(2):1208-1217. PubMed ID: 33434436
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. Structures and Dynamics of DNA Mini-Dumbbells Are Force Field Dependent.
    Winkler L; Galindo-Murillo R; Cheatham TE
    J Chem Theory Comput; 2023 Apr; 19(8):2198-2212. PubMed ID: 36976268
    [TBL] [Abstract][Full Text] [Related]  

  • 4. The impact of base stacking on the conformations and electrostatics of single-stranded DNA.
    Plumridge A; Meisburger SP; Andresen K; Pollack L
    Nucleic Acids Res; 2017 Apr; 45(7):3932-3943. PubMed ID: 28334825
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Theoretical Model for Solvent-Induced Base Stacking Interactions in Solvent-Free DNA Simulations.
    Mak CH
    J Phys Chem B; 2019 Mar; 123(9):1939-1949. PubMed ID: 30727734
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88.
    Zeng J; Li Y; Zhang JZ; Mei Y
    J Mol Model; 2016 Aug; 22(8):177. PubMed ID: 27392746
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Force field influences in beta-hairpin folding simulations.
    Lwin TZ; Luo R
    Protein Sci; 2006 Nov; 15(11):2642-55. PubMed ID: 17075138
    [TBL] [Abstract][Full Text] [Related]  

  • 8. AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations.
    Graen T; Hoefling M; Grubmüller H
    J Chem Theory Comput; 2014 Dec; 10(12):5505-12. PubMed ID: 26583233
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Atomistic Free Energy Model for Nucleic Acids: Simulations of Single-Stranded DNA and the Entropy Landscape of RNA Stem-Loop Structures.
    Mak CH
    J Phys Chem B; 2015 Nov; 119(47):14840-56. PubMed ID: 26548372
    [TBL] [Abstract][Full Text] [Related]  

  • 10. An improved DNA force field for ssDNA interactions with gold nanoparticles.
    Jiang X; Gao J; Huynh T; Huai P; Fan C; Zhou R; Song B
    J Chem Phys; 2014 Jun; 140(23):234102. PubMed ID: 24952518
    [TBL] [Abstract][Full Text] [Related]  

  • 11. How accurate are accurate force-fields for B-DNA?
    Dans PD; Ivani I; Hospital A; Portella G; González C; Orozco M
    Nucleic Acids Res; 2017 Apr; 45(7):4217-4230. PubMed ID: 28088759
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Are AMBER Force Fields and Implicit Solvation Models Additive? A Folding Study with a Balanced Peptide Test Set.
    Robinson MK; Monroe JI; Shell MS
    J Chem Theory Comput; 2016 Nov; 12(11):5631-5642. PubMed ID: 27731628
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Origin of overstretching transitions in single-stranded nucleic acids.
    Scholl ZN; Rabbi M; Lee D; Manson L; S-Gracz H; Marszalek PE
    Phys Rev Lett; 2013 Nov; 111(18):188302. PubMed ID: 24237568
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Force field development and simulations of intrinsically disordered proteins.
    Huang J; MacKerell AD
    Curr Opin Struct Biol; 2018 Feb; 48():40-48. PubMed ID: 29080468
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments.
    Grotz KK; Nueesch MF; Holmstrom ED; Heinz M; Stelzl LS; Schuler B; Hummer G
    J Phys Chem B; 2018 Dec; 122(49):11626-11639. PubMed ID: 30285443
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Ionic strength-dependent persistence lengths of single-stranded RNA and DNA.
    Chen H; Meisburger SP; Pabit SA; Sutton JL; Webb WW; Pollack L
    Proc Natl Acad Sci U S A; 2012 Jan; 109(3):799-804. PubMed ID: 22203973
    [TBL] [Abstract][Full Text] [Related]  

  • 17. A test of implicit solvent models on the folding simulation of the GB1 peptide.
    Shao Q; Yang L; Gao YQ
    J Chem Phys; 2009 May; 130(19):195104. PubMed ID: 19466868
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Exploring potentially alternative non-canonical DNA duplex structures through simulation.
    Galindo-Murillo R; Cheatham TE; Hopkins RC
    J Biomol Struct Dyn; 2019 Jun; 37(9):2201-2210. PubMed ID: 30047316
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles.
    Chan-Yao-Chong M; Durand D; Ha-Duong T
    J Chem Inf Model; 2019 May; 59(5):1743-1758. PubMed ID: 30840442
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering.
    Sim AY; Lipfert J; Herschlag D; Doniach S
    Phys Rev E Stat Nonlin Soft Matter Phys; 2012 Aug; 86(2 Pt 1):021901. PubMed ID: 23005779
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.