222 related articles for article (PubMed ID: 16449204)
1. Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study.
Cheng Y; Korolev N; Nordenskiöld L
Nucleic Acids Res; 2006; 34(2):686-96. PubMed ID: 16449204
[TBL] [Abstract][Full Text] [Related]
2. A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations.
Korolev N; Lyubartsev AP; Laaksonen A; Nordenskiöld L
Nucleic Acids Res; 2003 Oct; 31(20):5971-81. PubMed ID: 14530445
[TBL] [Abstract][Full Text] [Related]
3. Molecular dynamics simulation study of oriented polyamine- and Na-DNA: sequence specific interactions and effects on DNA structure.
Korolev N; Lyubartsev AP; Laaksonen A; Nordenskiöld L
Biopolymers; 2004 Apr; 73(5):542-55. PubMed ID: 15048778
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. On the competition between water, sodium ions, and spermine in binding to DNA: a molecular dynamics computer simulation study.
Korolev N; Lyubartsev AP; Laaksonen A; Nordenskiöld L
Biophys J; 2002 Jun; 82(6):2860-75. PubMed ID: 12023210
[TBL] [Abstract][Full Text] [Related]
6. A molecular dynamics simulation study of polyamine- and sodium-DNA. Interplay between polyamine binding and DNA structure.
Korolev N; Lyubartsev AP; Laaksonen A; Nordenskiöld L
Eur Biophys J; 2004 Dec; 33(8):671-82. PubMed ID: 15146298
[TBL] [Abstract][Full Text] [Related]
7. Hydration of counterions interacting with DNA double helix: a molecular dynamics study.
Perepelytsya S
J Mol Model; 2018 Jun; 24(7):171. PubMed ID: 29934661
[TBL] [Abstract][Full Text] [Related]
8. Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+).
Savelyev A; Papoian GA
J Am Chem Soc; 2006 Nov; 128(45):14506-18. PubMed ID: 17090034
[TBL] [Abstract][Full Text] [Related]
9. Molecular dynamics simulations of A. T-rich oligomers: sequence-specific binding of Na+ in the minor groove of B-DNA.
Mocci F; Saba G
Biopolymers; 2003 Apr; 68(4):471-85. PubMed ID: 12666173
[TBL] [Abstract][Full Text] [Related]
10. DNA structure: what's in charge?
McConnell KJ; Beveridge DL
J Mol Biol; 2000 Dec; 304(5):803-20. PubMed ID: 11124028
[TBL] [Abstract][Full Text] [Related]
11. H4 histone tail mediated DNA-DNA interaction and effects on DNA structure, flexibility, and counterion binding: a molecular dynamics study.
Korolev N; Nordenskiöld L
Biopolymers; 2007 Aug 5-15; 86(5-6):409-23. PubMed ID: 17471473
[TBL] [Abstract][Full Text] [Related]
12. Water and ion binding around r(UpA)12 and d(TpA)12 oligomers--comparison with RNA and DNA (CpG)12 duplexes.
Auffinger P; Westhof E
J Mol Biol; 2001 Feb; 305(5):1057-72. PubMed ID: 11162114
[TBL] [Abstract][Full Text] [Related]
13. Molecular dynamics simulations of DNA in solutions with different counter-ions.
Lyubartsev AP; Laaksonen A
J Biomol Struct Dyn; 1998 Dec; 16(3):579-92. PubMed ID: 10052615
[TBL] [Abstract][Full Text] [Related]
14. Spermine: an "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study.
Korolev N; Lyubartsev AP; Nordenskiöld L; Laaksonen A
J Mol Biol; 2001 May; 308(5):907-17. PubMed ID: 11352581
[TBL] [Abstract][Full Text] [Related]
15. Differential effects of oligosaccharides on the hydration of simple cations.
Eriksson M; Lindhorst TK; Hartke B
J Chem Phys; 2008 Mar; 128(10):105105. PubMed ID: 18345929
[TBL] [Abstract][Full Text] [Related]
16. Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?
Rueda M; Cubero E; Laughton CA; Orozco M
Biophys J; 2004 Aug; 87(2):800-11. PubMed ID: 15298889
[TBL] [Abstract][Full Text] [Related]
17. Water and ion binding around RNA and DNA (C,G) oligomers.
Auffinger P; Westhof E
J Mol Biol; 2000 Jul; 300(5):1113-31. PubMed ID: 10903858
[TBL] [Abstract][Full Text] [Related]
18. A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation.
Young MA; Ravishanker G; Beveridge DL
Biophys J; 1997 Nov; 73(5):2313-36. PubMed ID: 9370428
[TBL] [Abstract][Full Text] [Related]
19. Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding.
Csaszar K; Spacková N; Stefl R; Sponer J; Leontis NB
J Mol Biol; 2001 Nov; 313(5):1073-91. PubMed ID: 11700064
[TBL] [Abstract][Full Text] [Related]
20. Competitive substitution of hexammine cobalt(III) for Na+ and K+ ions in oriented DNA fibers.
Korolev N; Lyubartsev AP; Rupprecht A; Nordenskiöld L
Biopolymers; 2001 Mar; 58(3):268-78. PubMed ID: 11169387
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
