Cited by 359RNA and protein synthesis mechanismsAlgorithms and Data CompressionDNA and Biological Computing

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RNA Pseudoknot Prediction in Energy-Based Models

Lyngsø, Rune B., Pedersen, Christian N. S.·2000·Journal of Computational Biology

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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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Authors: Lyngsø, R. B., & Pedersen, C. N. S.
Affiliations: University of California, Santa Cruz (US)
Aarhus University (DK)
ORCID: Pedersen, Christian N. S.
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
DOI: 10.1089/106652700750050862
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
Licence: www.liebertpub.com/nv/resources-tools/text-and-data-mining-policy/121/ (tdm)
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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RNA Pseudoknot Prediction in Energy-Based Models

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