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A novel representation of RNA secondary structure based on element-contact graphs.

Shu W, Bo X, Zheng Z, Wang S.

BMC Bioinformatics. 2008 Apr 11;9:188.PMID: 18402706 [PubMed - indexed for MEDLINE]Related articlesFree article

Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.

Uzilov AV, Keegan JM, Mathews DH.

BMC Bioinformatics. 2006 Mar 27;7:173.PMID: 16566836 [PubMed - indexed for MEDLINE]Related articlesFree article

Candidates for novel RNA topologies.

Kim N, Shiffeldrim N, Gan HH, Schlick T.

J Mol Biol. 2004 Aug 27;341(5):1129-44.PMID: 15321711 [PubMed - indexed for MEDLINE]Related articles

Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design.

Gan HH, Pasquali S, Schlick T.

Nucleic Acids Res. 2003 Jun 1;31(11):2926-43.PMID: 12771219 [PubMed - indexed for MEDLINE]Related articlesFree article

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

Xue C, Li F, He T, Liu GP, Li Y, Zhang X.

BMC Bioinformatics. 2005 Dec 29;6:310.PMID: 16381612 [PubMed - indexed for MEDLINE]Related articlesFree article

Classification of non-coding RNA using graph representations of secondary structure.

Karklin Y, Meraz RF, Holbrook SR.

Pac Symp Biocomput. 2005:4-15.PMID: 15759609 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational methods in noncoding RNA research.

Machado-Lima A, del Portillo HA, Durham AM.

J Math Biol. 2008 Jan;56(1-2):15-49. Epub 2007 Sep 4. Review.PMID: 17786447 [PubMed - indexed for MEDLINE]Related articles

Directed acyclic graph kernels for structural RNA analysis.

Sato K, Mituyama T, Asai K, Sakakibara Y.

BMC Bioinformatics. 2008 Jul 22;9:318.PMID: 18647390 [PubMed - indexed for MEDLINE]Related articlesFree article

RAG: RNA-As-Graphs web resource.

Fera D, Kim N, Shiffeldrim N, Zorn J, Laserson U, Gan HH, Schlick T.

BMC Bioinformatics. 2004 Jul 6;5:88.PMID: 15238163 [PubMed - indexed for MEDLINE]Related articlesFree article

A statistical sampling algorithm for RNA secondary structure prediction.

Ding Y, Lawrence CE.

Nucleic Acids Res. 2003 Dec 15;31(24):7280-301.PMID: 14654704 [PubMed - indexed for MEDLINE]Related articlesFree article

A graph-topological approach to recognition of pattern and similarity in RNA secondary structures.

Benedetti G, Morosetti S.

Biophys Chem. 1996 Mar 7;59(1-2):179-84.PMID: 8867337 [PubMed - indexed for MEDLINE]Related articles

Analysis and classification of RNA tertiary structures.

Abraham M, Dror O, Nussinov R, Wolfson HJ.

RNA. 2008 Nov;14(11):2274-89. Epub 2008 Sep 29.PMID: 18824509 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification and classification of ncRNA molecules using graph properties.

Childs L, Nikoloski Z, May P, Walther D.

Nucleic Acids Res. 2009 May;37(9):e66. Epub 2009 Apr 1.PMID: 19339518 [PubMed - indexed for MEDLINE]Related articlesFree article

RNALogo: a new approach to display structural RNA alignment.

Chang TH, Horng JT, Huang HD.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W91-6. Epub 2008 May 21.PMID: 18495753 [PubMed - indexed for MEDLINE]Related articlesFree article

2D-RNA-coupling numbers: a new computational chemistry approach to link secondary structure topology with biological function.

González-Díaz H, Agüero-Chapin G, Varona J, Molina R, Delogu G, Santana L, Uriarte E, Podda G.

J Comput Chem. 2007 Apr 30;28(6):1049-56.PMID: 17279496 [PubMed - indexed for MEDLINE]Related articles

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.

Liu Q, Yang Y, Chen C, Bu J, Zhang Y, Ye X.

BMC Bioinformatics. 2008 Mar 31;9:176.PMID: 18373878 [PubMed - indexed for MEDLINE]Related articlesFree article

Natural/random protein classification models based on star network topological indices.

Munteanu CR, González-Díaz H, Borges F, de Magalhães AL.

J Theor Biol. 2008 Oct 21;254(4):775-83. Epub 2008 Jul 22.PMID: 18692072 [PubMed - indexed for MEDLINE]Related articles

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. Epub 2007 Aug 20.PMID: 17937495 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of the internal representations developed by neural networks for structures applied to quantitative structure--activity relationship studies of benzodiazepines.

Micheli A, Sperduti A, Starita A, Bianucci AM.

J Chem Inf Comput Sci. 2001 Jan-Feb;41(1):202-18.PMID: 11206375 [PubMed - indexed for MEDLINE]Related articles

Topological classification of RNA structures.

Bon M, Vernizzi G, Orland H, Zee A.

J Mol Biol. 2008 Jun 13;379(4):900-11. Epub 2008 Apr 18.PMID: 18485361 [PubMed - indexed for MEDLINE]Related articles