221 related articles for article (PubMed ID: 16698780)
1. Minor groove deformability of DNA: a molecular dynamics free energy simulation study.
Zacharias M
Biophys J; 2006 Aug; 91(3):882-91. PubMed ID: 16698780
[TBL] [Abstract][Full Text] [Related]
2. Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study.
Barthel A; Zacharias M
Biophys J; 2006 Apr; 90(7):2450-62. PubMed ID: 16399833
[TBL] [Abstract][Full Text] [Related]
3. Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein.
Pastor N; Pardo L; Weinstein H
Biophys J; 1997 Aug; 73(2):640-52. PubMed ID: 9251783
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. Binding of proteins to the minor groove of DNA: what are the structural and energetic determinants for kinking a basepair step?
Bosch D; Campillo M; Pardo L
J Comput Chem; 2003 Apr; 24(6):682-91. PubMed ID: 12666159
[TBL] [Abstract][Full Text] [Related]
6. Molecular dynamics simulations of B '-DNA: sequence effects on A-tract-induced bending and flexibility.
McConnell KJ; Beveridge DL
J Mol Biol; 2001 Nov; 314(1):23-40. PubMed ID: 11724529
[TBL] [Abstract][Full Text] [Related]
7. Binding mechanisms of TATA box-binding proteins: DNA kinking is stabilized by specific hydrogen bonds.
Pardo L; Campillo M; Bosch D; Pastor N; Weinstein H
Biophys J; 2000 Apr; 78(4):1988-96. PubMed ID: 10733977
[TBL] [Abstract][Full Text] [Related]
8. Dynamic simulations of 13 TATA variants refine kinetic hypotheses of sequence/activity relationships.
Qian X; Strahs D; Schlick T
J Mol Biol; 2001 May; 308(4):681-703. PubMed ID: 11350169
[TBL] [Abstract][Full Text] [Related]
9. What drives proteins into the major or minor grooves of DNA?
Privalov PL; Dragan AI; Crane-Robinson C; Breslauer KJ; Remeta DP; Minetti CA
J Mol Biol; 2007 Jan; 365(1):1-9. PubMed ID: 17055530
[TBL] [Abstract][Full Text] [Related]
10. Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations.
Giudice E; Várnai P; Lavery R
Nucleic Acids Res; 2003 Mar; 31(5):1434-43. PubMed ID: 12595551
[TBL] [Abstract][Full Text] [Related]
11. Anisotropy of B-DNA Groove Bending.
Ma N; van der Vaart A
J Am Chem Soc; 2016 Aug; 138(31):9951-8. PubMed ID: 27435602
[TBL] [Abstract][Full Text] [Related]
12. On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes.
Mukherjee A; Lavery R; Bagchi B; Hynes JT
J Am Chem Soc; 2008 Jul; 130(30):9747-55. PubMed ID: 18611009
[TBL] [Abstract][Full Text] [Related]
13. 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]
14. Solution structure of the calicheamicin gamma 1I-DNA complex.
Kumar RA; Ikemoto N; Patel DJ
J Mol Biol; 1997 Jan; 265(2):187-201. PubMed ID: 9020982
[TBL] [Abstract][Full Text] [Related]
15. Major versus minor groove DNA binding of a bisarginylporphyrin hybrid molecule: a molecular mechanics investigation.
Gresh N; Perrée-Fauvet M
J Comput Aided Mol Des; 1999 Mar; 13(2):123-37. PubMed ID: 10091119
[TBL] [Abstract][Full Text] [Related]
16. Effect of Zn2+ on DNA recognition and stability of the p53 DNA-binding domain.
Duan J; Nilsson L
Biochemistry; 2006 Jun; 45(24):7483-92. PubMed ID: 16768444
[TBL] [Abstract][Full Text] [Related]
17. B-DNA under stress: over- and untwisting of DNA during molecular dynamics simulations.
Kannan S; Kohlhoff K; Zacharias M
Biophys J; 2006 Oct; 91(8):2956-65. PubMed ID: 16861282
[TBL] [Abstract][Full Text] [Related]
18. Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study.
Samanta S; Raghunathan D; Mukherjee S
J Mol Graph Model; 2016 May; 66():9-19. PubMed ID: 27017424
[TBL] [Abstract][Full Text] [Related]
19. Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies.
Hamelberg D; Williams LD; Wilson WD
Nucleic Acids Res; 2002 Aug; 30(16):3615-23. PubMed ID: 12177304
[TBL] [Abstract][Full Text] [Related]
20. Molecular dynamics simulation in solvent of the estrogen receptor protein DNA binding domain in complex with a non-consensus estrogen response element DNA sequence.
Harris LF; Sullivan MR; Popken-Harris PD
J Biomol Struct Dyn; 1997 Dec; 15(3):407-30. PubMed ID: 9439992
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
