172 related articles for article (PubMed ID: 38780728)
1. RNA Secondary Structure Modeling Following the IPANEMAP Workflow.
Allouche D; De Bisschop G; Saaidi A; Hardouin P; du Moutier FL; Ponty Y; Bruno S
Methods Mol Biol; 2024; 2726():85-104. PubMed ID: 38780728
[TBL] [Abstract][Full Text] [Related]
2. IPANEMAP: integrative probing analysis of nucleic acids empowered by multiple accessibility profiles.
Saaidi A; Allouche D; Regnier M; Sargueil B; Ponty Y
Nucleic Acids Res; 2020 Sep; 48(15):8276-8289. PubMed ID: 32735675
[TBL] [Abstract][Full Text] [Related]
3. Advances and opportunities in RNA structure experimental determination and computational modeling.
Zhang J; Fei Y; Sun L; Zhang QC
Nat Methods; 2022 Oct; 19(10):1193-1207. PubMed ID: 36203019
[TBL] [Abstract][Full Text] [Related]
4. High-Throughput Nuclease Probing of RNA Structures Using FragSeq.
Uzilov AV; Underwood JG
Methods Mol Biol; 2016; 1490():105-34. PubMed ID: 27665596
[TBL] [Abstract][Full Text] [Related]
5. StructureFold2: Bringing chemical probing data into the computational fold of RNA structural analysis.
Tack DC; Tang Y; Ritchey LE; Assmann SM; Bevilacqua PC
Methods; 2018 Jul; 143():12-15. PubMed ID: 29410279
[TBL] [Abstract][Full Text] [Related]
6. Experiment-Assisted Secondary Structure Prediction with RNAstructure.
Xu ZZ; Mathews DH
Methods Mol Biol; 2016; 1490():163-76. PubMed ID: 27665598
[TBL] [Abstract][Full Text] [Related]
7. Predicting RNA SHAPE scores with deep learning.
Bliss N; Bindewald E; Shapiro BA
RNA Biol; 2020 Sep; 17(9):1324-1330. PubMed ID: 32476596
[TBL] [Abstract][Full Text] [Related]
8. Improving RNA secondary structure prediction with structure mapping data.
Sloma MF; Mathews DH
Methods Enzymol; 2015; 553():91-114. PubMed ID: 25726462
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. Modeling complex RNA tertiary folds with Rosetta.
Cheng CY; Chou FC; Das R
Methods Enzymol; 2015; 553():35-64. PubMed ID: 25726460
[TBL] [Abstract][Full Text] [Related]
11. Computational analysis of RNA structures with chemical probing data.
Ge P; Zhang S
Methods; 2015 Jun; 79-80():60-6. PubMed ID: 25687190
[TBL] [Abstract][Full Text] [Related]
12. iFoldRNA v2: folding RNA with constraints.
Krokhotin A; Houlihan K; Dokholyan NV
Bioinformatics; 2015 Sep; 31(17):2891-3. PubMed ID: 25910700
[TBL] [Abstract][Full Text] [Related]
13. RASP: an atlas of transcriptome-wide RNA secondary structure probing data.
Li P; Zhou X; Xu K; Zhang QC
Nucleic Acids Res; 2021 Jan; 49(D1):D183-D191. PubMed ID: 33068412
[TBL] [Abstract][Full Text] [Related]
14. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.
Wu Y; Shi B; Ding X; Liu T; Hu X; Yip KY; Yang ZR; Mathews DH; Lu ZJ
Nucleic Acids Res; 2015 Sep; 43(15):7247-59. PubMed ID: 26170232
[TBL] [Abstract][Full Text] [Related]
15. Direct identification of base-paired RNA nucleotides by correlated chemical probing.
Krokhotin A; Mustoe AM; Weeks KM; Dokholyan NV
RNA; 2017 Jan; 23(1):6-13. PubMed ID: 27803152
[TBL] [Abstract][Full Text] [Related]
16. Modeling and Predicting RNA Three-Dimensional Structures.
Reinharz V; Sarrazin-Gendron R; Waldispühl J
Methods Mol Biol; 2021; 2284():17-42. PubMed ID: 33835435
[TBL] [Abstract][Full Text] [Related]
17. RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.
Miao Z; Adamiak RW; Blanchet MF; Boniecki M; Bujnicki JM; Chen SJ; Cheng C; Chojnowski G; Chou FC; Cordero P; Cruz JA; Ferré-D'Amaré AR; Das R; Ding F; Dokholyan NV; Dunin-Horkawicz S; Kladwang W; Krokhotin A; Lach G; Magnus M; Major F; Mann TH; Masquida B; Matelska D; Meyer M; Peselis A; Popenda M; Purzycka KJ; Serganov A; Stasiewicz J; Szachniuk M; Tandon A; Tian S; Wang J; Xiao Y; Xu X; Zhang J; Zhao P; Zok T; Westhof E
RNA; 2015 Jun; 21(6):1066-84. PubMed ID: 25883046
[TBL] [Abstract][Full Text] [Related]
18. Automated RNA 3D Structure Prediction with RNAComposer.
Biesiada M; Purzycka KJ; Szachniuk M; Blazewicz J; Adamiak RW
Methods Mol Biol; 2016; 1490():199-215. PubMed ID: 27665601
[TBL] [Abstract][Full Text] [Related]
19. RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.
Piatkowski P; Kasprzak JM; Kumar D; Magnus M; Chojnowski G; Bujnicki JM
Methods Mol Biol; 2016; 1490():217-35. PubMed ID: 27665602
[TBL] [Abstract][Full Text] [Related]
20. GTfold: enabling parallel RNA secondary structure prediction on multi-core desktops.
Swenson MS; Anderson J; Ash A; Gaurav P; Sükösd Z; Bader DA; Harvey SC; Heitsch CE
BMC Res Notes; 2012 Jul; 5():341. PubMed ID: 22747589
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]