147 related articles for article (PubMed ID: 29113564)
1. Evaluating the quality of SHAPE data simulated by k-mers for RNA structure prediction.
Montaseri S; Zare-Mirakabad F; Ganjtabesh M
J Bioinform Comput Biol; 2017 Dec; 15(6):1750023. PubMed ID: 29113564
[TBL] [Abstract][Full Text] [Related]
2. Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data.
Montaseri S; Ganjtabesh M; Zare-Mirakabad F
PLoS One; 2016; 11(11):e0166965. PubMed ID: 27893832
[TBL] [Abstract][Full Text] [Related]
3. Integrating chemical footprinting data into RNA secondary structure prediction.
Zarringhalam K; Meyer MM; Dotu I; Chuang JH; Clote P
PLoS One; 2012; 7(10):e45160. PubMed ID: 23091593
[TBL] [Abstract][Full Text] [Related]
4. Mapping RNA Structure In Vitro with SHAPE Chemistry and Next-Generation Sequencing (SHAPE-Seq).
Watters KE; Lucks JB
Methods Mol Biol; 2016; 1490():135-62. PubMed ID: 27665597
[TBL] [Abstract][Full Text] [Related]
5. Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.
Smola MJ; Rice GM; Busan S; Siegfried NA; Weeks KM
Nat Protoc; 2015 Nov; 10(11):1643-69. PubMed ID: 26426499
[TBL] [Abstract][Full Text] [Related]
6. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.
Kirmizialtin S; Hennelly SP; Schug A; Onuchic JN; Sanbonmatsu KY
Methods Enzymol; 2015; 553():215-34. PubMed ID: 25726467
[TBL] [Abstract][Full Text] [Related]
7. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution.
Wilkinson KA; Merino EJ; Weeks KM
Nat Protoc; 2006; 1(3):1610-6. PubMed ID: 17406453
[TBL] [Abstract][Full Text] [Related]
8. K-partite RNA secondary structures.
Jiang M; Tejada PJ; Lasisi RO; Cheng S; Fechser DS
J Comput Biol; 2010 Jul; 17(7):915-25. PubMed ID: 20632871
[TBL] [Abstract][Full Text] [Related]
9. Improved free energy parameters for RNA pseudoknotted secondary structure prediction.
Andronescu MS; Pop C; Condon AE
RNA; 2010 Jan; 16(1):26-42. PubMed ID: 19933322
[TBL] [Abstract][Full Text] [Related]
10. RNA secondary structure prediction based on SHAPE data in helix regions.
Lotfi M; Zare-Mirakabad F; Montaseri S
J Theor Biol; 2015 Sep; 380():178-82. PubMed ID: 26037307
[TBL] [Abstract][Full Text] [Related]
11. Exploring RNA structural codes with SHAPE chemistry.
Weeks KM; Mauger DM
Acc Chem Res; 2011 Dec; 44(12):1280-91. PubMed ID: 21615079
[TBL] [Abstract][Full Text] [Related]
12. Asymptotic number of hairpins of saturated RNA secondary structures.
Clote P; Kranakis E; Krizanc D
Bull Math Biol; 2013 Dec; 75(12):2410-30. PubMed ID: 24142625
[TBL] [Abstract][Full Text] [Related]
13. Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.
Al-Khatib RM; Rashid NA; Abdullah R
J Biomol Struct Dyn; 2011 Aug; 29(1):1-26. PubMed ID: 21696223
[TBL] [Abstract][Full Text] [Related]
14. Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).
Watters KE; Yu AM; Strobel EJ; Settle AH; Lucks JB
Methods; 2016 Jul; 103():34-48. PubMed ID: 27064082
[TBL] [Abstract][Full Text] [Related]
15. Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data.
Tan Z; Sharma G; Mathews DH
Biophys J; 2017 Jul; 113(2):330-338. PubMed ID: 28735622
[TBL] [Abstract][Full Text] [Related]
16. Analysis of the RNA backbone: structural analysis of riboswitches by in-line probing and selective 2'-hydroxyl acylation and primer extension.
Wakeman CA; Winkler WC
Methods Mol Biol; 2009; 540():173-91. PubMed ID: 19381560
[TBL] [Abstract][Full Text] [Related]
17. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.
Hajdin CE; Bellaousov S; Huggins W; Leonard CW; Mathews DH; Weeks KM
Proc Natl Acad Sci U S A; 2013 Apr; 110(14):5498-503. PubMed ID: 23503844
[TBL] [Abstract][Full Text] [Related]
18. Prediction of RNA secondary structure by free energy minimization.
Mathews DH; Turner DH
Curr Opin Struct Biol; 2006 Jun; 16(3):270-8. PubMed ID: 16713706
[TBL] [Abstract][Full Text] [Related]
19. Computational prediction of RNA secondary structure.
Moss WN
Methods Enzymol; 2013; 530():3-65. PubMed ID: 24034313
[TBL] [Abstract][Full Text] [Related]
20. [Predicting RNA secondary structures including pseudoknots by covariance with stacking and minimum free energy].
Yang J; Luo Z; Fang X; Wang J; Tang K
Sheng Wu Gong Cheng Xue Bao; 2008 Apr; 24(4):659-64. PubMed ID: 18616179
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]