The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
A partition function algorithm for nucleic acid secondary structure including pseudoknots
Abstract
Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N5) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures. Hence, it is possible to determine the probability of sampling the lowest energy structure, or any other structure of particular interest. This capability motivates the use of the partition function for the design of DNA or RNA molecules for bioengineering applications. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1664–1677, 2003
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Cites
Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2700 · Cited by 3,795
Design and self-assembly of two-dimensional DNA crystals
Winfree, E., Liu, F., Wenzler, L. A., & Seeman, N. C. (1998) · Nature · doi:10.1038/28998 · Cited by 2,857
RNA Pseudoknot Prediction in Energy-Based Models
Lyngsø, R. B., & Pedersen, C. N. S. (2000) · Journal of Computational Biology · doi:10.1089/106652700750050862 · Cited by 359
Cited by
NUPACK: Analysis and design of nucleic acid systems
Zadeh, J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., Khan, A. R., Dirks, R. M., & Pierce, N. A. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21596 · Cited by 1,670
Self-citationTurner, D. H., & Mathews, D. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp892 · Cited by 575
Highly multiplexed in situ protein imaging with signal amplification by Immuno-SABER
Saka, S. K., Wang, Y., Kishi, J. Y., Zhu, A., Zeng, Y., Xie, W., Kirli, K., Yapp, C., Cicconet, M., Beliveau, B. J., et al. (2018) · doi:10.1101/507566 · Cited by 485
Using DNA to program the self-assembly of colloidal nanoparticles and microparticles
Rogers, W. B., Shih, W. M., & Manoharan, V. N. (2016) · Nature Reviews Materials · doi:10.1038/natrevmats.2016.8 · Cited by 361
Sato, K., Kato, Y., Hamada, M., Akutsu, T., & Asai, K. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr215 · Cited by 331
Metadata
- Authors
- Dirks, R. M., & Pierce, N. A.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 2003-08-13
- Volume
- 24
- Issue
- 13
- Pages
- 1664-1677
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2104141342
- Cited by
- 361
- References
- 3
- FWCI
- 5.47
- Type
- journal article
- Language
- en
- Open access
- closed
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