Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1373K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (53)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Yang, H.
Right arrow Articles by Westhof, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yang, H.
Right arrow Articles by Westhof, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 13 3450-3460
© 2003 Oxford University Press

Tools for the automatic identification and classification of RNA base pairs

Huanwang Yang, Fabrice Jossinet1, Neocles Leontis2, Li Chen, John Westbrook, Helen Berman and Eric Westhof1

Department of Chemistry and Chemical Biology, Rutgers University, NJ 08854-8087, USA 1 Institut de Biologie Moléculaire et Cellulaire du CNRS, Université Louis Pasteur, 15 Rue René Descartes, F-67084 Strasbourg Cedex, France 2 Chemistry Department, Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403, USA

*To whom correspondence should be addressed. Tel: +33 3 88 417046; Fax: +33 3 88 417066; Email: e.westhof{at}ibmc.u-strasbg.fr

Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson–Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 RNAHome page
M. Parisien, J. A. Cruz, E. Westhof, and F. Major
New metrics for comparing and assessing discrepancies between RNA 3D structures and models
RNA, October 1, 2009; 15(10): 1875 - 1885.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
W. Huang, J. Kim, S. Jha, and F. Aboul-ela
A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm
Nucleic Acids Res., October 1, 2009; 37(19): 6528 - 6539.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C.-E. Lai, M.-Y. Tsai, Y.-C. Liu, C.-W. Wang, K.-T. Chen, and C. L. Lu
FASTR3D: a fast and accurate search tool for similar RNA 3D structures
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W287 - W295.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
P. Zhou and Z. Shang
2D molecular graphics: a flattened world of chemistry and biology
Brief Bioinform, May 1, 2009; 10(3): 247 - 258.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
R. C. Spitale, A. T. Torelli, J. Krucinska, V. Bandarian, and J. E. Wedekind
The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain
J. Biol. Chem., April 24, 2009; 284(17): 11012 - 11016.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Smit, R. Knight, and J. Heringa
RNA structure prediction from evolutionary patterns of nucleotide composition
Nucleic Acids Res., April 1, 2009; 37(5): 1378 - 1386.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Stombaugh, C. L. Zirbel, E. Westhof, and N. B. Leontis
Frequency and isostericity of RNA base pairs
Nucleic Acids Res., April 1, 2009; 37(7): 2294 - 2312.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Xin and W. K. Olson
BPS: a database of RNA base-pair structures
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D83 - D88.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
M. Djelloul and A. Denise
Automated motif extraction and classification in RNA tertiary structures
RNA, December 1, 2008; 14(12): 2489 - 2497.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
Y. Xin, C. Laing, N. B. Leontis, and T. Schlick
Annotation of tertiary interactions in RNA structures reveals variations and correlations
RNA, December 1, 2008; 14(12): 2465 - 2477.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
M. Abraham, O. Dror, R. Nussinov, and H. J. Wolfson
Analysis and classification of RNA tertiary structures
RNA, November 1, 2008; 14(11): 2274 - 2289.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
S. Smit, K. Rother, J. Heringa, and R. Knight
From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal
RNA, March 1, 2008; 14(3): 410 - 416.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Popenda, M. Blazewicz, M. Szachniuk, and R. W. Adamiak
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D386 - D391.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. Bindewald, R. Hayes, Y. G. Yingling, W. Kasprzak, and B. A. Shapiro
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D392 - D397.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
A. Laederach
Informatics challenges in structured RNA
Brief Bioinform, September 1, 2007; 8(5): 294 - 303.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
E. Freyhult, V. Moulton, and P. Clote
Boltzmann probability of RNA structural neighbors and riboswitch detection
Bioinformatics, August 15, 2007; 23(16): 2054 - 2062.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Ferre, Y. Ponty, W. A. Lorenz, and P. Clote
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W659 - W668.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
A. T. Torelli, J. Krucinska, and J. E. Wedekind
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization
RNA, July 1, 2007; 13(7): 1052 - 1070.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
A. Laederach, J. M. Chan, A. Schwartzman, E. Willgohs, and R. B. Altman
Coplanar and coaxial orientations of RNA bases and helices
RNA, May 1, 2007; 13(5): 643 - 650.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Lescoute and E. Westhof
The interaction networks of structured RNAs
Nucleic Acids Res., December 2, 2006; 34(22): 6587 - 6604.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
S. D. Baird, M. Turcotte, R. G. Korneluk, and M. Holcik
Searching for IRES
RNA, October 1, 2006; 12(10): 1755 - 1785.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
O. Dror, R. Nussinov, and H. J. Wolfson
The ARTS web server for aligning RNA tertiary structures.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W412 - W415.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Hsiao, S. Mohan, E. Hershkovitz, A. Tannenbaum, and L. D. Williams
Single nucleotide RNA choreography
Nucleic Acids Res., March 10, 2006; 34(5): 1481 - 1491.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
A. LESCOUTE and E. WESTHOF
Topology of three-way junctions in folded RNAs.
RNA, January 1, 2006; 12(1): 83 - 93.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Lemieux and F. Major
Automated extraction and classification of RNA tertiary structure cyclic motifs.
Nucleic Acids Res., January 1, 2006; 34(8): 2340 - 2346.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
F. Jossinet and E. Westhof
Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure
Bioinformatics, August 1, 2005; 21(15): 3320 - 3321.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Lescoute, N. B. Leontis, C. Massire, and E. Westhof
Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments
Nucleic Acids Res., April 28, 2005; 33(8): 2395 - 2409.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
H.-C. HUANG, U. NAGASWAMY, and G. E. FOX
The application of cluster analysis in the intercomparison of loop structures in RNA
RNA, April 1, 2005; 11(4): 412 - 423.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Napierala, D. Michalowski, M. de Mezer, and W. J. Krzyzosiak
Facile FMR1 mRNA structure regulation by interruptions in CGG repeats
Nucleic Acids Res., January 19, 2005; 33(2): 451 - 463.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.