192 related articles for article (PubMed ID: 33902324)
21. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics.
Reeder J; Giegerich R
BMC Bioinformatics; 2004 Aug; 5():104. PubMed ID: 15294028
[TBL] [Abstract][Full Text] [Related]
22. Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots.
Song Y; Liu C; Malmberg RL; He C; Cai L
Int J Bioinform Res Appl; 2006; 2(3):289-304. PubMed ID: 18048167
[TBL] [Abstract][Full Text] [Related]
23. Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.
Xayaphoummine A; Bucher T; Thalmann F; Isambert H
Proc Natl Acad Sci U S A; 2003 Dec; 100(26):15310-5. PubMed ID: 14676318
[TBL] [Abstract][Full Text] [Related]
24. DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model.
Badelt S; Lorenz R; Hofacker IL
Bioinformatics; 2023 Jan; 39(1):. PubMed ID: 36655786
[TBL] [Abstract][Full Text] [Related]
25. In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding.
Incarnato D; Morandi E; Anselmi F; Simon LM; Basile G; Oliviero S
Nucleic Acids Res; 2017 Sep; 45(16):9716-9725. PubMed ID: 28934475
[TBL] [Abstract][Full Text] [Related]
26. New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation.
Antczak M; Popenda M; Zok T; Zurkowski M; Adamiak RW; Szachniuk M
Bioinformatics; 2018 Apr; 34(8):1304-1312. PubMed ID: 29236971
[TBL] [Abstract][Full Text] [Related]
27. Analysing RNA-kinetics based on folding space abstraction.
Huang J; Voß B
BMC Bioinformatics; 2014 Feb; 15():60. PubMed ID: 24575751
[TBL] [Abstract][Full Text] [Related]
28. Predicting RNA SHAPE scores with deep learning.
Bliss N; Bindewald E; Shapiro BA
RNA Biol; 2020 Sep; 17(9):1324-1330. PubMed ID: 32476596
[TBL] [Abstract][Full Text] [Related]
29. RNA folding on the 3D triangular lattice.
Gillespie J; Mayne M; Jiang M
BMC Bioinformatics; 2009 Nov; 10():369. PubMed ID: 19891777
[TBL] [Abstract][Full Text] [Related]
30. Energy-directed RNA structure prediction.
Hofacker IL
Methods Mol Biol; 2014; 1097():71-84. PubMed ID: 24639155
[TBL] [Abstract][Full Text] [Related]
31. A kinetic model of RNA folding.
Mironov AA; Lebedev VF
Biosystems; 1993; 30(1-3):49-56. PubMed ID: 7690611
[TBL] [Abstract][Full Text] [Related]
32. Effect of pausing on the cotranscriptional folding kinetics of RNAs.
Wang K; He Y; Shen Y; Wang Y; Xu X; Song X; Sun T
Int J Biol Macromol; 2022 Nov; 221():1345-1355. PubMed ID: 36115451
[TBL] [Abstract][Full Text] [Related]
33. RNA Visualization: Relevance and the Current State-of-the-Art Focusing on Pseudoknots.
Shabash B; Wiese KC
IEEE/ACM Trans Comput Biol Bioinform; 2017; 14(3):696-712. PubMed ID: 26915129
[TBL] [Abstract][Full Text] [Related]
34. [An iterative method for prediction of RNA secondary structures including pseudoknots based on minimum of free energy and covariance].
Wang ZX; Luo ZG; Guan NY; Yan FM; Jin X; Zhang W
Yi Chuan; 2007 Jul; 29(7):889-97. PubMed ID: 17646157
[TBL] [Abstract][Full Text] [Related]
35. Recent advances in RNA folding.
Fallmann J; Will S; Engelhardt J; Grüning B; Backofen R; Stadler PF
J Biotechnol; 2017 Nov; 261():97-104. PubMed ID: 28690134
[TBL] [Abstract][Full Text] [Related]
36. Prediction of RNA secondary structure with pseudoknots using integer programming.
Poolsap U; Kato Y; Akutsu T
BMC Bioinformatics; 2009 Jan; 10 Suppl 1(Suppl 1):S38. PubMed ID: 19208139
[TBL] [Abstract][Full Text] [Related]
37. Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots.
Kayedkhordeh M; Yamagami R; Bevilacqua PC; Mathews DH
Methods Mol Biol; 2021; 2167():113-143. PubMed ID: 32712918
[TBL] [Abstract][Full Text] [Related]
38. Fast folding of RNA pseudoknots initiated by laser temperature-jump.
Narayanan R; Velmurugu Y; Kuznetsov SV; Ansari A
J Am Chem Soc; 2011 Nov; 133(46):18767-74. PubMed ID: 21958201
[TBL] [Abstract][Full Text] [Related]
39. Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm.
Shapiro BA; Wu JC
Comput Appl Biosci; 1997 Aug; 13(4):459-71. PubMed ID: 9283762
[TBL] [Abstract][Full Text] [Related]
40. Crumple: a method for complete enumeration of all possible pseudoknot-free RNA secondary structures.
Bleckley S; Stone JW; Schroeder SJ
PLoS One; 2012; 7(12):e52414. PubMed ID: 23300665
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]