225 related articles for article (PubMed ID: 17507661)
1. Predicting helical coaxial stacking in RNA multibranch loops.
Tyagi R; Mathews DH
RNA; 2007 Jul; 13(7):939-51. PubMed ID: 17507661
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.
Mathews DH
RNA; 2004 Aug; 10(8):1178-90. PubMed ID: 15272118
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops.
Mathews DH; Turner DH
Biochemistry; 2002 Jan; 41(3):869-80. PubMed ID: 11790109
[TBL] [Abstract][Full Text] [Related]
6. Simultaneous prediction of RNA secondary structure and helix coaxial stacking.
Shareghi P; Wang Y; Malmberg R; Cai L
BMC Genomics; 2012 Jun; 13 Suppl 3(Suppl 3):S7. PubMed ID: 22759616
[TBL] [Abstract][Full Text] [Related]
7. 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]
8. Improved RNA secondary structure prediction by maximizing expected pair accuracy.
Lu ZJ; Gloor JW; Mathews DH
RNA; 2009 Oct; 15(10):1805-13. PubMed ID: 19703939
[TBL] [Abstract][Full Text] [Related]
9. Predicting protein-binding RNA nucleotides with consideration of binding partners.
Tuvshinjargal N; Lee W; Park B; Han K
Comput Methods Programs Biomed; 2015 Jun; 120(1):3-15. PubMed ID: 25907142
[TBL] [Abstract][Full Text] [Related]
10. [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]
11. 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]
12. 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]
13. A two-length-scale polymer theory for RNA loop free energies and helix stacking.
Aalberts DP; Nandagopal N
RNA; 2010 Jul; 16(7):1350-5. PubMed ID: 20504955
[TBL] [Abstract][Full Text] [Related]
14. Predicting coaxial helical stacking in RNA junctions.
Laing C; Wen D; Wang JT; Schlick T
Nucleic Acids Res; 2012 Jan; 40(2):487-98. PubMed ID: 21917853
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. Thermodynamics of three-way multibranch loops in RNA.
Diamond JM; Turner DH; Mathews DH
Biochemistry; 2001 Jun; 40(23):6971-81. PubMed ID: 11389613
[TBL] [Abstract][Full Text] [Related]
17. 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]
18. 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]
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. Prediction of RNA secondary structure by maximizing pseudo-expected accuracy.
Hamada M; Sato K; Asai K
BMC Bioinformatics; 2010 Nov; 11():586. PubMed ID: 21118522
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]