312 related articles for article (PubMed ID: 29107980)
1. Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.
Sloma MF; Mathews DH
PLoS Comput Biol; 2017 Nov; 13(11):e1005827. PubMed ID: 29107980
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. 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]
4. 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]
5. RNA structure and dynamics: a base pairing perspective.
Halder S; Bhattacharyya D
Prog Biophys Mol Biol; 2013 Nov; 113(2):264-83. PubMed ID: 23891726
[TBL] [Abstract][Full Text] [Related]
6. Modeling RNA secondary structure folding ensembles using SHAPE mapping data.
Spasic A; Assmann SM; Bevilacqua PC; Mathews DH
Nucleic Acids Res; 2018 Jan; 46(1):314-323. PubMed ID: 29177466
[TBL] [Abstract][Full Text] [Related]
7. New in silico approach to assessing RNA secondary structures with non-canonical base pairs.
Rybarczyk A; Szostak N; Antczak M; Zok T; Popenda M; Adamiak R; Blazewicz J; Szachniuk M
BMC Bioinformatics; 2015 Sep; 16(1):276. PubMed ID: 26329823
[TBL] [Abstract][Full Text] [Related]
8. Classification and Identification of Non-canonical Base Pairs and Structural Motifs.
Sarrazin-Gendron R; Waldispühl J; Reinharz V
Methods Mol Biol; 2024; 2726():143-168. PubMed ID: 38780731
[TBL] [Abstract][Full Text] [Related]
9. RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs.
Antczak M; Zablocki M; Zok T; Rybarczyk A; Blazewicz J; Szachniuk M
Bioinformatics; 2019 Jan; 35(1):152-155. PubMed ID: 29985979
[TBL] [Abstract][Full Text] [Related]
10. AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure.
DiChiacchio L; Sloma MF; Mathews DH
Bioinformatics; 2016 Apr; 32(7):1033-9. PubMed ID: 26589271
[TBL] [Abstract][Full Text] [Related]
11. TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.
Tan Z; Fu Y; Sharma G; Mathews DH
Nucleic Acids Res; 2017 Nov; 45(20):11570-11581. PubMed ID: 29036420
[TBL] [Abstract][Full Text] [Related]
12. Non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis.
Das J; Mukherjee S; Mitra A; Bhattacharyya D
J Biomol Struct Dyn; 2006 Oct; 24(2):149-61. PubMed ID: 16928138
[TBL] [Abstract][Full Text] [Related]
13. A folding algorithm for extended RNA secondary structures.
Höner zu Siederdissen C; Bernhart SH; Stadler PF; Hofacker IL
Bioinformatics; 2011 Jul; 27(13):i129-36. PubMed ID: 21685061
[TBL] [Abstract][Full Text] [Related]
14. Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework.
Loyer G; Reinharz V
Bioinformatics; 2024 Feb; 40(2):. PubMed ID: 38230755
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. Structures of non-canonical tandem base pairs in RNA helices: review.
Heus HA; Hilbers CW
Nucleosides Nucleotides Nucleic Acids; 2003; 22(5-8):559-71. PubMed ID: 14565230
[TBL] [Abstract][Full Text] [Related]
17. Prediction of Secondary Structures Conserved in Multiple RNA Sequences.
Xu ZZ; Mathews DH
Methods Mol Biol; 2016; 1490():35-50. PubMed ID: 27665591
[TBL] [Abstract][Full Text] [Related]
18. Accurate prediction of RNA nucleotide interactions with backbone k-tree model.
Ding L; Xue X; LaMarca S; Mohebbi M; Samad A; Malmberg RL; Cai L
Bioinformatics; 2015 Aug; 31(16):2660-7. PubMed ID: 25886978
[TBL] [Abstract][Full Text] [Related]
19. 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]
20. 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]
[Next] [New Search]
