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RNA Pseudoknot Prediction in Energy-Based Models
Abstract
RNA molecules are sequences of nucleotides that serve as more than mere intermediaries between DNA and proteins, e.g., as catalytic molecules. Computational prediction of RNA secondary structure is among the few structure prediction problems that can be solved satisfactorily in polynomial time. Most work has been done to predict structures that do not contain pseudoknots. Allowing pseudoknots introduces modeling and computational problems. In this paper we consider the problem of predicting RNA secondary structures with pseudoknots based on free energy minimization. We first give a brief comparison of energy-based methods for predicting RNA secondary structures with pseudoknots. We then prove that the general problem of predicting RNA secondary structures containing pseudoknots is NP complete for a large class of reasonable models of pseudoknots.
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“Moreover, predicting structures with pseudoknots is classified as an NP-complete problem [5].”
From Towards secondary structure prediction of longer mRNA sequences using a quantum-centric optimization scheme (2025) · cites this paper as [5]
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Metadata
- Authors
- Lyngsø, R. B., & Pedersen, C. N. S.
- Affiliations
- University of California, Santa Cruz (US)
- Aarhus University (DK)
- Venue
- Journal of Computational Biology
- Publisher
- SAGE Publications
- Published
- 2000-08
- Volume
- 7
- Issue
- 3-4
- Pages
- 409-427
- ISSN
- 1066-5277 (ISSN-L)
- 1557-8666
- OpenAlex
- W2076756368
- Cited by
- 359
- References
- 28
- Citations by year
- 2026: 4 · 2025: 3 · 2024: 25 · 2023: 8 · 2022: 27 · 2021: 9 · 2020: 8 · 2019: 9 · 2018: 11 · 2017: 10 · 2016: 11 · 2015: 13 · 2014: 11 · 2013: 16 · 2012: 21
- FWCI
- 1.33
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Computational Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
- Physical Sciences › Mathematics › Theoretical Computer Science › DNA and Biological Computing
- Keywords
- RNA pseudoknots, RNA secondary structure prediction, energy-based models, free energy minimization, NP-completeness, computational complexity
- MeSH terms
- Algorithms, Models, Molecular, Nucleic Acid Conformation, RNA, Thermodynamics, Computational Biology
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