247 related articles for article (PubMed ID: 28334976)
1. A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction.
Zuber J; Sun H; Zhang X; McFadyen I; Mathews DH
Nucleic Acids Res; 2017 Jun; 45(10):6168-6176. PubMed ID: 28334976
[TBL] [Abstract][Full Text] [Related]
2. Estimating uncertainty in predicted folding free energy changes of RNA secondary structures.
Zuber J; Mathews DH
RNA; 2019 Jun; 25(6):747-754. PubMed ID: 30952689
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation.
Lu ZJ; Turner DH; Mathews DH
Nucleic Acids Res; 2006; 34(17):4912-24. PubMed ID: 16982646
[TBL] [Abstract][Full Text] [Related]
5. Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures.
Sloma MF; Mathews DH
RNA; 2016 Dec; 22(12):1808-1818. PubMed ID: 27852924
[TBL] [Abstract][Full Text] [Related]
6. Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.
Zuber J; Schroeder SJ; Sun H; Turner DH; Mathews DH
Nucleic Acids Res; 2022 May; 50(9):5251-5262. PubMed ID: 35524574
[TBL] [Abstract][Full Text] [Related]
7. TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.
Harmanci AO; Sharma G; Mathews DH
BMC Bioinformatics; 2011 Apr; 12():108. PubMed ID: 21507242
[TBL] [Abstract][Full Text] [Related]
8. A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation.
Layton DM; Bundschuh R
Nucleic Acids Res; 2005; 33(2):519-24. PubMed ID: 15673712
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. Thermodynamic characterization of single mismatches found in naturally occurring RNA.
Davis AR; Znosko BM
Biochemistry; 2007 Nov; 46(46):13425-36. PubMed ID: 17958380
[TBL] [Abstract][Full Text] [Related]
11. Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction.
Doshi KJ; Cannone JJ; Cobaugh CW; Gutell RR
BMC Bioinformatics; 2004 Aug; 5():105. PubMed ID: 15296519
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. RNA Secondary Structure Prediction Based on Energy Models.
Akiyama M; Sato K
Methods Mol Biol; 2023; 2586():89-105. PubMed ID: 36705900
[TBL] [Abstract][Full Text] [Related]
14. Thermodynamic characterization of RNA duplexes containing naturally occurring 1 x 2 nucleotide internal loops.
Badhwar J; Karri S; Cass CK; Wunderlich EL; Znosko BM
Biochemistry; 2007 Dec; 46(50):14715-24. PubMed ID: 18020450
[TBL] [Abstract][Full Text] [Related]
15. Asymptotic distribution of motifs in a stochastic context-free grammar model of RNA folding.
Poznanović S; Heitsch CE
J Math Biol; 2014 Dec; 69(6-7):1743-72. PubMed ID: 24384698
[TBL] [Abstract][Full Text] [Related]
16. Secondary Structure Prediction of Single Sequences Using RNAstructure.
Xu ZZ; Mathews DH
Methods Mol Biol; 2016; 1490():15-34. PubMed ID: 27665590
[TBL] [Abstract][Full Text] [Related]
17. 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]
18. 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]
19. Sequence dependence of the stability of RNA hairpin molecules with six nucleotide loops.
Vecenie CJ; Morrow CV; Zyra A; Serra MJ
Biochemistry; 2006 Feb; 45(5):1400-7. PubMed ID: 16445282
[TBL] [Abstract][Full Text] [Related]
20. 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]
[Next] [New Search]