149 related articles for article (PubMed ID: 30047316)
1. 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]
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. Hydrophobic unnatural base pairs show a Watson-Crick pairing in micro-second molecular dynamics simulations.
Galindo-Murillo R; Barroso-Flores J
J Biomol Struct Dyn; 2020 Sep; 38(14):4098-4106. PubMed ID: 31542995
[TBL] [Abstract][Full Text] [Related]
4. Molecular dynamics analysis of stabilities of the telomeric Watson-Crick duplex and the associated i-motif as a function of pH and temperature.
Panczyk T; Wolski P
Biophys Chem; 2018 Jun; 237():22-30. PubMed ID: 29631151
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. [Analysis of Conformational Features of Watson-Crick Duplex Fragments by Molecular Mechanics and Quantum Mechanics Methods].
Poltev VI; Anisimov VM; Sanchez C; Deriabina A; Gonzalez E; Garcia D; Rivas F; Polteva NA
Biofizika; 2016; 61(2):259-69. PubMed ID: 27192827
[TBL] [Abstract][Full Text] [Related]
7. Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations.
Jin H; Zheng S; Wang Z; Luo C; Shen J; Jiang H; Zhang L; Zhang L
J Mol Model; 2006 Sep; 12(6):781-91. PubMed ID: 16450112
[TBL] [Abstract][Full Text] [Related]
8. Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA.
Cubero E; Luque FJ; Orozco M
Biophys J; 2006 Feb; 90(3):1000-8. PubMed ID: 16287814
[TBL] [Abstract][Full Text] [Related]
9. Evidence for a new Z-type left-handed DNA helix: properties of Z(WC)-DNA.
Ansevin AT; Wang AH
Nucleic Acids Res; 1990 Oct; 18(20):6119-26. PubMed ID: 2235494
[TBL] [Abstract][Full Text] [Related]
10. Simulation of DNA double-strand dissociation and formation during replica-exchange molecular dynamics simulations.
Kannan S; Zacharias M
Phys Chem Chem Phys; 2009 Dec; 11(45):10589-95. PubMed ID: 20145803
[TBL] [Abstract][Full Text] [Related]
11. DNA stretching and compression: large-scale simulations of double helical structures.
Kosikov KM; Gorin AA; Zhurkin VB; Olson WK
J Mol Biol; 1999 Jun; 289(5):1301-26. PubMed ID: 10373369
[TBL] [Abstract][Full Text] [Related]
12. The contribution of DNA single-stranded order to the thermodynamics of duplex formation.
Vesnaver G; Breslauer KJ
Proc Natl Acad Sci U S A; 1991 May; 88(9):3569-73. PubMed ID: 2023903
[TBL] [Abstract][Full Text] [Related]
13. pH and cation effects on the properties of parallel pyrimidine motif DNA triplexes.
Sugimoto N; Wu P; Hara H; Kawamoto Y
Biochemistry; 2001 Aug; 40(31):9396-405. PubMed ID: 11478909
[TBL] [Abstract][Full Text] [Related]
14. Transition between B-DNA and Z-DNA: free energy landscape for the B-Z junction propagation.
Lee J; Kim YG; Kim KK; Seok C
J Phys Chem B; 2010 Aug; 114(30):9872-81. PubMed ID: 20666528
[TBL] [Abstract][Full Text] [Related]
15. Computational Probing of Watson-Crick/Hoogsteen Breathing in a DNA Duplex Containing N1-Methylated Adenine.
Yang C; Kim E; Lim M; Pak Y
J Chem Theory Comput; 2019 Jan; 15(1):751-761. PubMed ID: 30501194
[TBL] [Abstract][Full Text] [Related]
16. Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex.
Cubero E; Abrescia NG; Subirana JA; Luque FJ; Orozco M
J Am Chem Soc; 2003 Nov; 125(47):14603-12. PubMed ID: 14624611
[TBL] [Abstract][Full Text] [Related]
17. Symmetrization of the backbone of nucleic acids: a molecular dynamics study.
Pant P; Pathak A; Jayaram B
J Biomol Struct Dyn; 2020 Feb; 38(3):673-681. PubMed ID: 30821653
[TBL] [Abstract][Full Text] [Related]
18. The first example of a Hoogsteen base-paired DNA duplex in dynamic equilibrium with a Watson-Crick base-paired duplex--a structural (NMR), kinetic and thermodynamic study.
Isaksson J; Zamaratski E; Maltseva TV; Agback P; Kumar A; Chattopadhyaya J
J Biomol Struct Dyn; 2001 Jun; 18(6):783-806. PubMed ID: 11444368
[TBL] [Abstract][Full Text] [Related]
19. Molecular mechanics simulations on covalent complexes of mitomycin C and its analogues with left-handed DNA duplexes.
Rao SN; Iyengar BS; Wunz TP; Remers WA
J Med Chem; 1991 Dec; 34(12):3380-8. PubMed ID: 1766002
[TBL] [Abstract][Full Text] [Related]
20. Molecular dynamics investigations of DNA triple helical models: unique features of the Watson-Crick duplex.
Sekharudu CY; Yathindra N; Sundaralingam M
J Biomol Struct Dyn; 1993 Oct; 11(2):225-44. PubMed ID: 8286053
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]