87 related articles for article (PubMed ID: 19899145)
1. RNA secondary structure prediction using a self-consistent mean field approach.
Kleesiek J; Torda AE
J Comput Chem; 2010 Apr; 31(6):1135-42. PubMed ID: 19899145
[TBL] [Abstract][Full Text] [Related]
2. Partition function and base pairing probabilities for RNA-RNA interaction prediction.
Huang FW; Qin J; Reidys CM; Stadler PF
Bioinformatics; 2009 Oct; 25(20):2646-54. PubMed ID: 19671692
[TBL] [Abstract][Full Text] [Related]
3. [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]
4. Revolutions in RNA secondary structure prediction.
Mathews DH
J Mol Biol; 2006 Jun; 359(3):526-32. PubMed ID: 16500677
[TBL] [Abstract][Full Text] [Related]
5. Robust prediction of consensus secondary structures using averaged base pairing probability matrices.
Kiryu H; Kin T; Asai K
Bioinformatics; 2007 Feb; 23(4):434-41. PubMed ID: 17182698
[TBL] [Abstract][Full Text] [Related]
6. The energetics of small internal loops in RNA.
Schroeder SJ; Burkard ME; Turner DH
Biopolymers; 1999-2000; 52(4):157-67. PubMed ID: 11295748
[TBL] [Abstract][Full Text] [Related]
7. Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations.
Mládek A; Sharma P; Mitra A; Bhattacharyya D; Sponer J; Sponer JE
J Phys Chem B; 2009 Feb; 113(6):1743-55. PubMed ID: 19152254
[TBL] [Abstract][Full Text] [Related]
8. Rfold: an exact algorithm for computing local base pairing probabilities.
Kiryu H; Kin T; Asai K
Bioinformatics; 2008 Feb; 24(3):367-73. PubMed ID: 18056736
[TBL] [Abstract][Full Text] [Related]
9. Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model.
Zacharias M; Sklenar H
J Mol Biol; 1999 Jun; 289(2):261-75. PubMed ID: 10366504
[TBL] [Abstract][Full Text] [Related]
10. Predicting a set of minimal free energy RNA secondary structures common to two sequences.
Mathews DH
Bioinformatics; 2005 May; 21(10):2246-53. PubMed ID: 15731207
[TBL] [Abstract][Full Text] [Related]
11. An RNA folding algorithm including pseudoknots based on dynamic weighted matching.
Liu H; Xu D; Shao J; Wang Y
Comput Biol Chem; 2006 Feb; 30(1):72-6. PubMed ID: 16321572
[TBL] [Abstract][Full Text] [Related]
12. 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]
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. On the algebraic representation of RNA secondary structures with G x U pairs.
Casasnovas J; Miro-Julia J; Rosselló F
J Math Biol; 2003 Jul; 47(1):1-22. PubMed ID: 12827446
[TBL] [Abstract][Full Text] [Related]
15. Extracting stacking interaction parameters for RNA from the data set of native structures.
Dima RI; Hyeon C; Thirumalai D
J Mol Biol; 2005 Mar; 347(1):53-69. PubMed ID: 15733917
[TBL] [Abstract][Full Text] [Related]
16. Secondary structure prediction of interacting RNA molecules.
Andronescu M; Zhang ZC; Condon A
J Mol Biol; 2005 Feb; 345(5):987-1001. PubMed ID: 15644199
[TBL] [Abstract][Full Text] [Related]
17. Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?
Svozil D; Hobza P; Sponer J
J Phys Chem B; 2010 Jan; 114(2):1191-203. PubMed ID: 20000584
[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. Irreducibility in RNA structures.
Jin EY; Reidys CM
Bull Math Biol; 2010 Feb; 72(2):375-99. PubMed ID: 19890676
[TBL] [Abstract][Full Text] [Related]
20. Prediction of consensus RNA secondary structures including pseudoknots.
Witwer C; Hofacker IL; Stadler PF
IEEE/ACM Trans Comput Biol Bioinform; 2004; 1(2):66-77. PubMed ID: 17048382
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]