460 related articles for article (PubMed ID: 25910700)
1. 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]
2. iFoldRNA: three-dimensional RNA structure prediction and folding.
Sharma S; Ding F; Dokholyan NV
Bioinformatics; 2008 Sep; 24(17):1951-2. PubMed ID: 18579566
[TBL] [Abstract][Full Text] [Related]
3. INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints.
Busch A; Backofen R
Nucleic Acids Res; 2007 Jul; 35(Web Server issue):W310-3. PubMed ID: 17452349
[TBL] [Abstract][Full Text] [Related]
4. Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models.
Krokhotin A; Dokholyan NV
Methods Enzymol; 2015; 553():65-89. PubMed ID: 25726461
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. 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]
7. Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities.
Hagio T; Sakuraba S; Iwakiri J; Mori R; Asai K
BMC Bioinformatics; 2018 Feb; 19(Suppl 1):38. PubMed ID: 29504917
[TBL] [Abstract][Full Text] [Related]
8. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.
Washietl S; Bernhart SH; Kellis M
Methods Mol Biol; 2014; 1097():125-41. PubMed ID: 24639158
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. 3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction.
Wang J; Wang J; Huang Y; Xiao Y
Int J Mol Sci; 2019 Aug; 20(17):. PubMed ID: 31450739
[TBL] [Abstract][Full Text] [Related]
11. The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures.
Gruber AR; Neuböck R; Hofacker IL; Washietl S
Nucleic Acids Res; 2007 Jul; 35(Web Server issue):W335-8. PubMed ID: 17452347
[TBL] [Abstract][Full Text] [Related]
12. Structure clustering features on the Sfold Web server.
Chan CY; Lawrence CE; Ding Y
Bioinformatics; 2005 Oct; 21(20):3926-8. PubMed ID: 16109749
[TBL] [Abstract][Full Text] [Related]
13. incaRNAfbinv: a web server for the fragment-based design of RNA sequences.
Drory Retwitzer M; Reinharz V; Ponty Y; Waldispühl J; Barash D
Nucleic Acids Res; 2016 Jul; 44(W1):W308-14. PubMed ID: 27185893
[TBL] [Abstract][Full Text] [Related]
14. HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures.
He J; Wang J; Tao H; Xiao Y; Huang SY
Nucleic Acids Res; 2019 Jul; 47(W1):W35-W42. PubMed ID: 31114906
[TBL] [Abstract][Full Text] [Related]
15. Memory efficient folding algorithms for circular RNA secondary structures.
Hofacker IL; Stadler PF
Bioinformatics; 2006 May; 22(10):1172-6. PubMed ID: 16452114
[TBL] [Abstract][Full Text] [Related]
16. RADAR: a web server for RNA data analysis and research.
Khaladkar M; Bellofatto V; Wang JT; Tian B; Shapiro BA
Nucleic Acids Res; 2007 Jul; 35(Web Server issue):W300-4. PubMed ID: 17517784
[TBL] [Abstract][Full Text] [Related]
17. Three-dimensional RNA structure refinement by hydroxyl radical probing.
Ding F; Lavender CA; Weeks KM; Dokholyan NV
Nat Methods; 2012 Apr; 9(6):603-8. PubMed ID: 22504587
[TBL] [Abstract][Full Text] [Related]
18. Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities.
Mokdad A; Leontis NB
Bioinformatics; 2006 Sep; 22(17):2168-70. PubMed ID: 16820430
[TBL] [Abstract][Full Text] [Related]
19. CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures.
Islam S; Ge P; Zhang S
Nucleic Acids Res; 2017 Aug; 45(14):e136. PubMed ID: 28641399
[TBL] [Abstract][Full Text] [Related]
20. How to benchmark RNA secondary structure prediction accuracy.
Mathews DH
Methods; 2019 Jun; 162-163():60-67. PubMed ID: 30951834
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]