130 related articles for article (PubMed ID: 37166444)
1. High-quality, customizable heuristics for RNA 3D structure alignment.
Zurkowski M; Antczak M; Szachniuk M
Bioinformatics; 2023 May; 39(5):. PubMed ID: 37166444
[TBL] [Abstract][Full Text] [Related]
2. RNAhugs web server for customized 3D RNA structure alignment.
Zurkowski M; Swiercz M; Wozny F; Antczak M; Szachniuk M
Nucleic Acids Res; 2024 Jul; 52(W1):W348-W353. PubMed ID: 38587206
[TBL] [Abstract][Full Text] [Related]
3. RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA.
Gong S; Zhang C; Zhang Y
Bioinformatics; 2019 Nov; 35(21):4459-4461. PubMed ID: 31161212
[TBL] [Abstract][Full Text] [Related]
4. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions.
Rahrig RR; Leontis NB; Zirbel CL
Bioinformatics; 2010 Nov; 26(21):2689-97. PubMed ID: 20929913
[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. DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model.
Badelt S; Lorenz R; Hofacker IL
Bioinformatics; 2023 Jan; 39(1):. PubMed ID: 36655786
[TBL] [Abstract][Full Text] [Related]
7. R3D-BLAST2: an improved search tool for similar RNA 3D substructures.
Yen CY; Lin JC; Chen KT; Lu CL
BMC Bioinformatics; 2017 Dec; 18(Suppl 16):574. PubMed ID: 29297283
[TBL] [Abstract][Full Text] [Related]
8. iPARTS: an improved tool of pairwise alignment of RNA tertiary structures.
Wang CW; Chen KT; Lu CL
Nucleic Acids Res; 2010 Jul; 38(Web Server issue):W340-7. PubMed ID: 20507908
[TBL] [Abstract][Full Text] [Related]
9. RNA structural alignments, part I: Sankoff-based approaches for structural alignments.
Havgaard JH; Gorodkin J
Methods Mol Biol; 2014; 1097():275-90. PubMed ID: 24639164
[TBL] [Abstract][Full Text] [Related]
10. Vargas: heuristic-free alignment for assessing linear and graph read aligners.
Darby CA; Gaddipati R; Schatz MC; Langmead B
Bioinformatics; 2020 Jun; 36(12):3712-3718. PubMed ID: 32321164
[TBL] [Abstract][Full Text] [Related]
11. LCS-TA to identify similar fragments in RNA 3D structures.
Wiedemann J; Zok T; Milostan M; Szachniuk M
BMC Bioinformatics; 2017 Oct; 18(1):456. PubMed ID: 29058576
[TBL] [Abstract][Full Text] [Related]
12. rMSA: A Sequence Search and Alignment Algorithm to Improve RNA Structure Modeling.
Zhang C; Zhang Y; Pyle AM
J Mol Biol; 2023 Jul; 435(14):167904. PubMed ID: 37356900
[TBL] [Abstract][Full Text] [Related]
13. A method for aligning RNA secondary structures and its application to RNA motif detection.
Liu J; Wang JT; Hu J; Tian B
BMC Bioinformatics; 2005 Apr; 6():89. PubMed ID: 15817128
[TBL] [Abstract][Full Text] [Related]
14. ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures.
Tagashira M; Asai K
Bioinformatics; 2022 Jan; 38(3):710-719. PubMed ID: 34694364
[TBL] [Abstract][Full Text] [Related]
15. The ARTS web server for aligning RNA tertiary structures.
Dror O; Nussinov R; Wolfson HJ
Nucleic Acids Res; 2006 Jul; 34(Web Server issue):W412-5. PubMed ID: 16845038
[TBL] [Abstract][Full Text] [Related]
16. 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; WaldispĆ¼hl J
Bioinformatics; 2012 Jun; 28(12):i207-14. PubMed ID: 22689763
[TBL] [Abstract][Full Text] [Related]
17. SARSA: a web tool for structural alignment of RNA using a structural alphabet.
Chang YF; Huang YL; Lu CL
Nucleic Acids Res; 2008 Jul; 36(Web Server issue):W19-24. PubMed ID: 18502774
[TBL] [Abstract][Full Text] [Related]
18. RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models.
Huang H; Lin Z; He D; Hong L; Li Y
Bioinformatics; 2024 Jun; 40(Supplement_1):i347-i356. PubMed ID: 38940178
[TBL] [Abstract][Full Text] [Related]
19. RNA 3D structure prediction: (1) assessing rna 3D structure similarity from 2D structure similarity.
Barreda D C JE; Shigenobu Y; Ichiishi E; Del Carpio M CA
Genome Inform; 2004; 15(2):112-20. PubMed ID: 15706497
[TBL] [Abstract][Full Text] [Related]
20. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix.
Havgaard JH; Torarinsson E; Gorodkin J
PLoS Comput Biol; 2007 Oct; 3(10):1896-908. PubMed ID: 17937495
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]