148 related articles for article (PubMed ID: 26130723)
1. Identifying novel sequence variants of RNA 3D motifs.
Zirbel CL; Roll J; Sweeney BA; Petrov AI; Pirrung M; Leontis NB
Nucleic Acids Res; 2015 Sep; 43(15):7504-20. PubMed ID: 26130723
[TBL] [Abstract][Full Text] [Related]
2. JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
Roll J; Zirbel CL; Sweeney B; Petrov AI; Leontis N
Nucleic Acids Res; 2016 Jul; 44(W1):W320-7. PubMed ID: 27235417
[TBL] [Abstract][Full Text] [Related]
3. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.
Petrov AI; Zirbel CL; Leontis NB
RNA; 2013 Oct; 19(10):1327-40. PubMed ID: 23970545
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.
Sarver M; Zirbel CL; Stombaugh J; Mokdad A; Leontis NB
J Math Biol; 2008 Jan; 56(1-2):215-52. PubMed ID: 17694311
[TBL] [Abstract][Full Text] [Related]
6. Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments.
Lescoute A; Leontis NB; Massire C; Westhof E
Nucleic Acids Res; 2005; 33(8):2395-409. PubMed ID: 15860776
[TBL] [Abstract][Full Text] [Related]
7. 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]
8. CONTRAfold: RNA secondary structure prediction without physics-based models.
Do CB; Woods DA; Batzoglou S
Bioinformatics; 2006 Jul; 22(14):e90-8. PubMed ID: 16873527
[TBL] [Abstract][Full Text] [Related]
9. Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules.
Leontis NB; Stombaugh J; Westhof E
Biochimie; 2002 Sep; 84(9):961-73. PubMed ID: 12458088
[TBL] [Abstract][Full Text] [Related]
10. RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data.
Yao J; Reinharz V; Major F; Waldispühl J
Nucleic Acids Res; 2017 Jul; 45(W1):W440-W444. PubMed ID: 28525607
[TBL] [Abstract][Full Text] [Related]
11. Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions.
Kauffmann AD; Kennedy SD; Zhao J; Turner DH
Biochemistry; 2017 Jul; 56(29):3733-3744. PubMed ID: 28700212
[TBL] [Abstract][Full Text] [Related]
12. Frequency and isostericity of RNA base pairs.
Stombaugh J; Zirbel CL; Westhof E; Leontis NB
Nucleic Acids Res; 2009 Apr; 37(7):2294-312. PubMed ID: 19240142
[TBL] [Abstract][Full Text] [Related]
13. Sequence-based identification of 3D structural modules in RNA with RMDetect.
Cruz JA; Westhof E
Nat Methods; 2011 Jun; 8(6):513-21. PubMed ID: 21552257
[TBL] [Abstract][Full Text] [Related]
14. Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.
Matsui H; Sato K; Sakakibara Y
Proc IEEE Comput Syst Bioinform Conf; 2004; ():290-9. PubMed ID: 16448022
[TBL] [Abstract][Full Text] [Related]
15. Modeling RNA tertiary structure motifs by graph-grammars.
St-Onge K; Thibault P; Hamel S; Major F
Nucleic Acids Res; 2007; 35(5):1726-36. PubMed ID: 17317683
[TBL] [Abstract][Full Text] [Related]
16. DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities.
Ferrè F; Ponty Y; Lorenz WA; Clote P
Nucleic Acids Res; 2007 Jul; 35(Web Server issue):W659-68. PubMed ID: 17567620
[TBL] [Abstract][Full Text] [Related]
17. WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs.
Petrov AI; Zirbel CL; Leontis NB
Nucleic Acids Res; 2011 Jul; 39(Web Server issue):W50-5. PubMed ID: 21515634
[TBL] [Abstract][Full Text] [Related]
18. RNAMotifScanX: a graph alignment approach for RNA structural motif identification.
Zhong C; Zhang S
RNA; 2015 Mar; 21(3):333-46. PubMed ID: 25595715
[TBL] [Abstract][Full Text] [Related]
19. Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.
Matsui H; Sato K; Sakakibara Y
Bioinformatics; 2005 Jun; 21(11):2611-7. PubMed ID: 15784748
[TBL] [Abstract][Full Text] [Related]
20. Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop.
Havrila M; Réblová K; Zirbel CL; Leontis NB; Šponer J
J Phys Chem B; 2013 Nov; 117(46):14302-19. PubMed ID: 24144333
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
