212 related articles for article (PubMed ID: 21889515)
1. Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure.
Gardner DP; Ren P; Ozer S; Gutell RR
J Mol Biol; 2011 Oct; 413(2):473-83. PubMed ID: 21889515
[TBL] [Abstract][Full Text] [Related]
2. Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.
Wu JC; Gardner DP; Ozer S; Gutell RR; Ren P
J Mol Biol; 2009 Aug; 391(4):769-83. PubMed ID: 19540243
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. 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]
5. Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure.
Reinharz V; Major F; Waldispühl J
Bioinformatics; 2012 Jun; 28(12):i207-14. PubMed ID: 22689763
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.
Parlea LG; Sweeney BA; Hosseini-Asanjan M; Zirbel CL; Leontis NB
Methods; 2016 Jul; 103():99-119. PubMed ID: 27125735
[TBL] [Abstract][Full Text] [Related]
8. Exact learning of RNA energy parameters from structure.
Chitsaz H; Aminisharifabad M
J Comput Biol; 2015 Jun; 22(6):463-73. PubMed ID: 25756654
[TBL] [Abstract][Full Text] [Related]
9. Evaluation of a sophisticated SCFG design for RNA secondary structure prediction.
Nebel ME; Scheid A
Theory Biosci; 2011 Dec; 130(4):313-36. PubMed ID: 22135038
[TBL] [Abstract][Full Text] [Related]
10. Thermodynamic characterization of RNA 2 × 3 nucleotide internal loops.
Hausmann NZ; Znosko BM
Biochemistry; 2012 Jul; 51(26):5359-68. PubMed ID: 22720720
[TBL] [Abstract][Full Text] [Related]
11. 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]
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. 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]
14. 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]
15. Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
Klosterman PS; Hendrix DK; Tamura M; Holbrook SR; Brenner SE
Nucleic Acids Res; 2004; 32(8):2342-52. PubMed ID: 15121895
[TBL] [Abstract][Full Text] [Related]
16. Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments.
Seemann SE; Gorodkin J; Backofen R
Nucleic Acids Res; 2008 Nov; 36(20):6355-62. PubMed ID: 18836192
[TBL] [Abstract][Full Text] [Related]
17. ISFOLD: structure prediction of base pairs in non-helical RNA motifs from isostericity signatures in their sequence alignments.
Mokdad A; Frankel AD
J Biomol Struct Dyn; 2008 Apr; 25(5):467-72. PubMed ID: 18282001
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Stochastic modeling of RNA pseudoknotted structures: a grammatical approach.
Cai L; Malmberg RL; Wu Y
Bioinformatics; 2003; 19 Suppl 1():i66-73. PubMed ID: 12855439
[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]
