168 related articles for article (PubMed ID: 26613316)
1. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN Internal Loops Studied by Molecular Dynamics Methods.
Réblová K; Střelcová Z; Kulhánek P; Beššeová I; Mathews DH; Van Nostrand K; Yildirim I; Turner DH; Šponer J
J Chem Theory Comput; 2010 Mar; 6(3):910-29. PubMed ID: 26613316
[TBL] [Abstract][Full Text] [Related]
2. An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods.
Réblová K; Střelcová Z; Kulhánek P; Beššeová I; Mathews DH; Nostrand KV; Yildirim I; Turner DH; Sponer J
J Chem Theory Comput; 2010 Jan; 2010(6):910-929. PubMed ID: 21132104
[TBL] [Abstract][Full Text] [Related]
3. The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits.
Shankar N; Kennedy SD; Chen G; Krugh TR; Turner DH
Biochemistry; 2006 Oct; 45(39):11776-89. PubMed ID: 17002278
[TBL] [Abstract][Full Text] [Related]
4. A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis.
Réblová K; Šponer JE; Špačková N; Beššeová I; Šponer J
J Phys Chem B; 2011 Dec; 115(47):13897-910. PubMed ID: 21999672
[TBL] [Abstract][Full Text] [Related]
5. The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions.
Lee JC; Gutell RR; Russell R
J Mol Biol; 2006 Jul; 360(5):978-88. PubMed ID: 16828489
[TBL] [Abstract][Full Text] [Related]
6. Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view.
Sponer JE; Réblova K; Mokdad A; Sychrovský V; Leszczynski J; Sponer J
J Phys Chem B; 2007 Aug; 111(30):9153-64. PubMed ID: 17602515
[TBL] [Abstract][Full Text] [Related]
7. Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation.
Spasic A; Kennedy SD; Needham L; Manoharan M; Kierzek R; Turner DH; Mathews DH
RNA; 2018 May; 24(5):656-672. PubMed ID: 29434035
[TBL] [Abstract][Full Text] [Related]
8. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields.
Fadrná E; Špačková N; Sarzyñska J; Koča J; Orozco M; Cheatham TE; Kulinski T; Šponer J
J Chem Theory Comput; 2009 Sep; 5(9):2514-30. PubMed ID: 26616629
[TBL] [Abstract][Full Text] [Related]
9. Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change.
Van Nostrand KP; Kennedy SD; Turner DH; Mathews DH
J Chem Theory Comput; 2011 Nov; 7(11):3779-3792. PubMed ID: 22116780
[TBL] [Abstract][Full Text] [Related]
10. RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA.
Hammond NB; Tolbert BS; Kierzek R; Turner DH; Kennedy SD
Biochemistry; 2010 Jul; 49(27):5817-27. PubMed ID: 20481618
[TBL] [Abstract][Full Text] [Related]
11. Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs.
Sponer J; Mokdad A; Sponer JE; Spacková N; Leszczynski J; Leontis NB
J Mol Biol; 2003 Jul; 330(5):967-78. PubMed ID: 12860120
[TBL] [Abstract][Full Text] [Related]
12. The lonepair triloop: a new motif in RNA structure.
Lee JC; Cannone JJ; Gutell RR
J Mol Biol; 2003 Jan; 325(1):65-83. PubMed ID: 12473452
[TBL] [Abstract][Full Text] [Related]
13. A DNA hairpin with a single residue loop closed by a strongly distorted Watson-Crick G x C base-pair.
El Amri C; Mauffret O; Monnot M; Tevanian G; Lescot E; Porumb H; Fermandjian S
J Mol Biol; 1999 Nov; 294(2):427-42. PubMed ID: 10610769
[TBL] [Abstract][Full Text] [Related]
14. RNA tertiary structure of the HIV RRE domain II containing non-Watson-Crick base pairs GG and GA: molecular modeling studies.
Le SY; Pattabiraman N; Maizel JV
Nucleic Acids Res; 1994 Sep; 22(19):3966-76. PubMed ID: 7937119
[TBL] [Abstract][Full Text] [Related]
15. The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.
Leontis NB; Westhof E
RNA; 1998 Sep; 4(9):1134-53. PubMed ID: 9740131
[TBL] [Abstract][Full Text] [Related]
16. Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs.
Yildirim I; Stern HA; Sponer J; Spackova N; Turner DH
J Chem Theory Comput; 2009 Aug; 5(8):2088-2100. PubMed ID: 20090924
[TBL] [Abstract][Full Text] [Related]
17. Structural dynamics of the box C/D RNA kink-turn and its complex with proteins: the role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations.
Spacková N; Réblová K; Sponer J
J Phys Chem B; 2010 Aug; 114(32):10581-93. PubMed ID: 20701388
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Dependence of A-RNA simulations on the choice of the force field and salt strength.
Besseová I; Otyepka M; Réblová K; Sponer J
Phys Chem Chem Phys; 2009 Dec; 11(45):10701-11. PubMed ID: 20145814
[TBL] [Abstract][Full Text] [Related]
20. Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules.
Leontis NB; Stombaugh J; Westhof E
Biochimie; 2002 Sep; 84(9):961-73. PubMed ID: 12458088
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
