The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.
Tools for the automatic identification and classification of RNA base pairs
Open accessAbstract
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/.
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Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,578
Principles of Nucleic Acid Structure
(2008) · Elsevier eBooks · doi:10.1016/b978-0-12-369507-9.x5001-8 · Cited by 4,504
Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., et al. (1979) · Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry · doi:10.1107/s0567740879009249 · Cited by 1,167
Geometric nomenclature and classification of RNA base pairs
LEONTIS, N. B., & WESTHOF, E. (2001) · RNA · doi:10.1017/s1355838201002515 · Cited by 1,073
Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S. H., Srinivasan, A. R., & Schneider, B. (1992) · Biophysical Journal · doi:10.1016/s0006-3495(92)81649-1 · Cited by 1,003
Three-dimensional structure of a hammerhead ribozyme
Pley, H. W., Flaherty, K. M., & McKay, D. B. (1994) · Nature · doi:10.1038/372068a0 · Cited by 953
Oubridge, C., Ito, N., Evans, P. R., Teo, C.-H., & Nagai, K. (1994) · Nature · doi:10.1038/372432a0 · Cited by 831
The non-Watson-Crick base pairs and their associated isostericity matrices
Leontis, N. B. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf481 · Cited by 796
Crystal structure of a hepatitis delta virus ribozyme
Ferré-D'Amaré, A. R., Zhou, K., & Doudna, J. A. (1998) · Nature · doi:10.1038/26912 · Cited by 785
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Hsiao, C., Lenz, T. K., Peters, J. K., Fang, P.-Y., Schneider, D. M., Anderson, E. J., Preeprem, T., Bowman, J. C., O'Neill, E. B., Lie, L., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt023 · Cited by 45
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Metadata
- Authors
- Yang, H.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-07-01
- Volume
- 31
- Issue
- 13
- Pages
- 3450-3460
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2091705944
- Cited by
- 286
- References
- 54
- FWCI
- 3.43
- Type
- journal article
- Language
- en
- Open access
- bronze
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