BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

207 related articles for article (PubMed ID: 21059937)

  • 1. Chemically accurate coarse graining of double-stranded DNA.
    Savelyev A; Papoian GA
    Proc Natl Acad Sci U S A; 2010 Nov; 107(47):20340-5. PubMed ID: 21059937
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Molecular renormalization group coarse-graining of electrolyte solutions: application to aqueous NaCl and KCl.
    Savelyev A; Papoian GA
    J Phys Chem B; 2009 Jun; 113(22):7785-93. PubMed ID: 19425537
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Modeling DNA Flexibility: Comparison of Force Fields from Atomistic to Multiscale Levels.
    Minhas V; Sun T; Mirzoev A; Korolev N; Lyubartsev AP; Nordenskiöld L
    J Phys Chem B; 2020 Jan; 124(1):38-49. PubMed ID: 31805230
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA.
    Savelyev A; Papoian GA
    Biophys J; 2009 May; 96(10):4044-52. PubMed ID: 19450476
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Do monovalent mobile ions affect DNA's flexibility at high salt content?
    Savelyev A
    Phys Chem Chem Phys; 2012 Feb; 14(7):2250-4. PubMed ID: 22246071
    [TBL] [Abstract][Full Text] [Related]  

  • 6. A coarse-grained model of DNA with explicit solvation by water and ions.
    DeMille RC; Cheatham TE; Molinero V
    J Phys Chem B; 2011 Jan; 115(1):132-42. PubMed ID: 21155552
    [TBL] [Abstract][Full Text] [Related]  

  • 7. A coarse-grained simulation study of the structures, energetics, and dynamics of linear and circular DNA with its ions.
    Naômé A; Laaksonen A; Vercauteren DP
    J Chem Theory Comput; 2015 Jun; 11(6):2813-26. PubMed ID: 26575574
    [TBL] [Abstract][Full Text] [Related]  

  • 8. A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality.
    Morriss-Andrews A; Rottler J; Plotkin SS
    J Chem Phys; 2010 Jan; 132(3):035105. PubMed ID: 20095755
    [TBL] [Abstract][Full Text] [Related]  

  • 9. A coarse-grain three-site-per-nucleotide model for DNA with explicit ions.
    Freeman GS; Hinckley DM; de Pablo JJ
    J Chem Phys; 2011 Oct; 135(16):165104. PubMed ID: 22047269
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Is DNA's rigidity dominated by electrostatic or nonelectrostatic interactions?
    Savelyev A; Materese CK; Papoian GA
    J Am Chem Soc; 2011 Dec; 133(48):19290-3. PubMed ID: 22039974
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.
    Takada S; Kanada R; Tan C; Terakawa T; Li W; Kenzaki H
    Acc Chem Res; 2015 Dec; 48(12):3026-35. PubMed ID: 26575522
    [TBL] [Abstract][Full Text] [Related]  

  • 12. From rigid base pairs to semiflexible polymers: coarse-graining DNA.
    Becker NB; Everaers R
    Phys Rev E Stat Nonlin Soft Matter Phys; 2007 Aug; 76(2 Pt 1):021923. PubMed ID: 17930081
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Coarse-grained ions without charges: reproducing the solvation structure of NaCl in water using short-ranged potentials.
    DeMille RC; Molinero V
    J Chem Phys; 2009 Jul; 131(3):034107. PubMed ID: 19624181
    [TBL] [Abstract][Full Text] [Related]  

  • 14. The "sugar" coarse-grained DNA model.
    Kovaleva NA; Koroleva Kikot IP; Mazo MA; Zubova EA
    J Mol Model; 2017 Feb; 23(2):66. PubMed ID: 28185115
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Coarse-Grained Ions for Nucleic Acid Modeling.
    Hinckley DM; de Pablo JJ
    J Chem Theory Comput; 2015 Nov; 11(11):5436-46. PubMed ID: 26574332
    [TBL] [Abstract][Full Text] [Related]  

  • 16. DNA overstretching transition: ionic strength effects.
    Punkkinen O; Hansen PL; Miao L; Vattulainen I
    Biophys J; 2005 Aug; 89(2):967-78. PubMed ID: 15923227
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Recent advances in transferable coarse-grained modeling of proteins.
    Kar P; Feig M
    Adv Protein Chem Struct Biol; 2014; 96():143-80. PubMed ID: 25443957
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations.
    Wassenaar TA; Ingólfsson HI; Priess M; Marrink SJ; Schäfer LV
    J Phys Chem B; 2013 Apr; 117(13):3516-30. PubMed ID: 23406326
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Brownian dynamics of double-stranded DNA in periodic systems with discrete salt.
    Mielke SP; Grønbech-Jensen N; Benham CJ
    Phys Rev E Stat Nonlin Soft Matter Phys; 2008 Mar; 77(3 Pt 1):031924. PubMed ID: 18517439
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.
    Assenza S; Pérez R
    J Chem Theory Comput; 2022 May; 18(5):3239-3256. PubMed ID: 35394775
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.