152 related articles for article (PubMed ID: 38780729)
1. How Parameters Influence SHAPE-Directed Predictions.
Greenwood T; Heitsch CE
Methods Mol Biol; 2024; 2726():105-124. PubMed ID: 38780729
[TBL] [Abstract][Full Text] [Related]
2. Analysis of energy-based algorithms for RNA secondary structure prediction.
Hajiaghayi M; Condon A; Hoos HH
BMC Bioinformatics; 2012 Feb; 13():22. PubMed ID: 22296803
[TBL] [Abstract][Full Text] [Related]
3. The determination of RNA folding nearest neighbor parameters.
Andronescu M; Condon A; Turner DH; Mathews DH
Methods Mol Biol; 2014; 1097():45-70. PubMed ID: 24639154
[TBL] [Abstract][Full Text] [Related]
4. Classified Dynamic Programming in RNA Structure Analysis.
Voß B
Methods Mol Biol; 2024; 2726():125-141. PubMed ID: 38780730
[TBL] [Abstract][Full Text] [Related]
5. A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.
Rivas E; Lang R; Eddy SR
RNA; 2012 Feb; 18(2):193-212. PubMed ID: 22194308
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. RnaPredict--an evolutionary algorithm for RNA secondary structure prediction.
Wiese K; Deschenes A; Hendriks A
IEEE/ACM Trans Comput Biol Bioinform; 2008; 5(1):25-41. PubMed ID: 18245873
[TBL] [Abstract][Full Text] [Related]
8. VarGibbs Usage in the Optimization of Nearest-Neighbor Parameters and Prediction of Melting Temperature of RNA Duplexes.
Ferreira I; Weber G
Methods Mol Biol; 2024; 2726():15-43. PubMed ID: 38780726
[TBL] [Abstract][Full Text] [Related]
9. Thermodynamic matchers: strengthening the significance of RNA folding energies.
Höchsmann T; Höchsmann M; Giegerich R
Comput Syst Bioinformatics Conf; 2006; ():111-21. PubMed ID: 17369630
[TBL] [Abstract][Full Text] [Related]
10. Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction.
Zuber J; Cabral BJ; McFadyen I; Mauger DM; Mathews DH
RNA; 2018 Nov; 24(11):1568-1582. PubMed ID: 30104207
[TBL] [Abstract][Full Text] [Related]
11. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure.
Turner DH; Mathews DH
Nucleic Acids Res; 2010 Jan; 38(Database issue):D280-2. PubMed ID: 19880381
[TBL] [Abstract][Full Text] [Related]
12. Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction.
von Löhneysen S; Spicher T; Varenyk Y; Yao HT; Lorenz R; Hofacker I; Stadler PF
J Comput Biol; 2024 Jun; 31(6):549-563. PubMed ID: 38935442
[TBL] [Abstract][Full Text] [Related]
13. The challenge of RNA branching prediction: a parametric analysis of multiloop initiation under thermodynamic optimization.
Poznanović S; Barrera-Cruz F; Kirkpatrick A; Ielusic M; Heitsch C
J Struct Biol; 2020 Apr; 210(1):107475. PubMed ID: 32032754
[TBL] [Abstract][Full Text] [Related]
14. Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides.
Hudson GA; Bloomingdale RJ; Znosko BM
RNA; 2013 Nov; 19(11):1474-82. PubMed ID: 24062573
[TBL] [Abstract][Full Text] [Related]
15. Thermodynamics of RNA structures by Wang-Landau sampling.
Lou F; Clote P
Bioinformatics; 2010 Jun; 26(12):i278-86. PubMed ID: 20529917
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. 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]
18. GTfold: enabling parallel RNA secondary structure prediction on multi-core desktops.
Swenson MS; Anderson J; Ash A; Gaurav P; Sükösd Z; Bader DA; Harvey SC; Heitsch CE
BMC Res Notes; 2012 Jul; 5():341. PubMed ID: 22747589
[TBL] [Abstract][Full Text] [Related]
19. Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.
Spasic A; Berger KD; Chen JL; Seetin MG; Turner DH; Mathews DH
Nucleic Acids Res; 2018 Jun; 46(10):4883-4892. PubMed ID: 29718397
[TBL] [Abstract][Full Text] [Related]
20. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.
Washietl S; Bernhart SH; Kellis M
Methods Mol Biol; 2014; 1097():125-41. PubMed ID: 24639158
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]