239 related articles for article (PubMed ID: 25805858)
1. Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin.
Giambaşu GM; York DM; Case DA
RNA; 2015 May; 21(5):963-74. PubMed ID: 25805858
[TBL] [Abstract][Full Text] [Related]
2. Free energy profile of RNA hairpins: a molecular dynamics simulation study.
Deng NJ; Cieplak P
Biophys J; 2010 Feb; 98(4):627-36. PubMed ID: 20159159
[TBL] [Abstract][Full Text] [Related]
3. Molecular dynamics simulation of the structure, dynamics, and thermostability of the RNA hairpins uCACGg and cUUCGg.
Villa A; Widjajakusuma E; Stock G
J Phys Chem B; 2008 Jan; 112(1):134-42. PubMed ID: 18069816
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model.
Williams DJ; Hall KB
Biophys J; 1999 Jun; 76(6):3192-205. PubMed ID: 10354444
[TBL] [Abstract][Full Text] [Related]
6. Experimental and computational studies of the G[UUCG]C RNA tetraloop.
Williams DJ; Hall KB
J Mol Biol; 2000 Apr; 297(5):1045-61. PubMed ID: 10764572
[TBL] [Abstract][Full Text] [Related]
7. Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations.
Kannan S; Zacharias M
Biophys J; 2007 Nov; 93(9):3218-28. PubMed ID: 17660316
[TBL] [Abstract][Full Text] [Related]
8. UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations.
Mráziková K; Mlýnský V; Kührová P; Pokorná P; Kruse H; Krepl M; Otyepka M; Banáš P; Šponer J
J Chem Theory Comput; 2020 Dec; 16(12):7601-7617. PubMed ID: 33215915
[TBL] [Abstract][Full Text] [Related]
9. The crystal structure of UUCG tetraloop.
Ennifar E; Nikulin A; Tishchenko S; Serganov A; Nevskaya N; Garber M; Ehresmann B; Ehresmann C; Nikonov S; Dumas P
J Mol Biol; 2000 Nov; 304(1):35-42. PubMed ID: 11071808
[TBL] [Abstract][Full Text] [Related]
10. Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.
Smith LG; Tan Z; Spasic A; Dutta D; Salas-Estrada LA; Grossfield A; Mathews DH
J Chem Theory Comput; 2018 Dec; 14(12):6598-6612. PubMed ID: 30375860
[TBL] [Abstract][Full Text] [Related]
11. Integrating NMR and simulations reveals motions in the UUCG tetraloop.
Bottaro S; Nichols PJ; Vögeli B; Parrinello M; Lindorff-Larsen K
Nucleic Acids Res; 2020 Jun; 48(11):5839-5848. PubMed ID: 32427326
[TBL] [Abstract][Full Text] [Related]
12. A molecular dynamics simulation of the flavin mononucleotide-RNA aptamer complex.
Schneider C; Sühnel J
Biopolymers; 1999 Sep; 50(3):287-302. PubMed ID: 10397790
[TBL] [Abstract][Full Text] [Related]
13. Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.
Banáš P; Hollas D; Zgarbová M; Jurečka P; Orozco M; Cheatham TE; Šponer J; Otyepka M
J Chem Theory Comput; 2010 Dec; 6(12):3836-3849. PubMed ID: 35283696
[TBL] [Abstract][Full Text] [Related]
14. Dynamics and stability of GCAA tetraloops with 2-aminopurine and purine substitutions.
Sarzynska J; Kulinski T
J Biomol Struct Dyn; 2005 Feb; 22(4):425-39. PubMed ID: 15588106
[TBL] [Abstract][Full Text] [Related]
15. Accuracy of MD solvent models in RNA structure refinement assessed via liquid-crystal NMR and spin relaxation data.
Bergonzo C; Grishaev A
J Struct Biol; 2019 Sep; 207(3):250-259. PubMed ID: 31279068
[TBL] [Abstract][Full Text] [Related]
16. RNA stability under different combinations of amber force fields and solvation models.
Gong Z; Xiao Y; Xiao Y
J Biomol Struct Dyn; 2010 Dec; 28(3):431-41. PubMed ID: 20919758
[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. Structure and dynamics of an RNA tetraloop: a joint molecular dynamics and NMR study.
Koplin J; Mu Y; Richter C; Schwalbe H; Stock G
Structure; 2005 Sep; 13(9):1255-67. PubMed ID: 16154083
[TBL] [Abstract][Full Text] [Related]
19. Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop.
Li W; Ma B; Shapiro B
J Biomol Struct Dyn; 2001 Dec; 19(3):381-96. PubMed ID: 11790138
[TBL] [Abstract][Full Text] [Related]
20. RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop.
Sorin EJ; Engelhardt MA; Herschlag D; Pande VS
J Mol Biol; 2002 Apr; 317(4):493-506. PubMed ID: 11955005
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]