Adventures with RNA graphs

The structure of RNA has been a natural subject for mathematical modeling, inviting many innovative computational frameworks. This single-stranded polynucleotide chain can fold upon itself in numerous ways to form hydrogen-bonded segments, imperfect with single-stranded loops. Illustrating these pai...

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Vydáno v:Methods (San Diego, Calif.) Ročník 143; s. 16 - 33
Hlavní autor: Schlick, Tamar
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States Elsevier Inc 01.07.2018
Témata:
Algorithms
Coarse-grained modeling
Computational Biology - instrumentation
Computational Biology - methods
Databases, Nucleic Acid
Graphs
hydrogen bonding
Mathematical biology
mathematical models
Models, Molecular
Nucleic Acid Conformation
prediction
RNA
RNA - chemistry
RNA - genetics
RNA design
RNA secondary structure
RNA structure
Graphs
Mathematical biology
Coarse-grained modeling
RNA design
RNA structure
RNA secondary structure
ISSN:1046-2023, 1095-9130, 1095-9130
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Shrnutí:The structure of RNA has been a natural subject for mathematical modeling, inviting many innovative computational frameworks. This single-stranded polynucleotide chain can fold upon itself in numerous ways to form hydrogen-bonded segments, imperfect with single-stranded loops. Illustrating these paired and non-paired interaction networks, known as RNA’s secondary (2D) structure, using mathematical graph objects has been illuminating for RNA structure analysis. Building upon such seminal work from the 1970s and 1980s, graph models are now used to study not only RNA structure but also describe RNA’s recurring modular units, sample the conformational space accessible to RNAs, predict RNA’s three-dimensional folds, and apply the combined aspects to novel RNA design. In this article, we outline the development of the RNA-As-Graphs (or RAG) approach and highlight current applications to RNA structure prediction and design.
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ISSN:1046-2023
1095-9130
1095-9130
DOI:10.1016/j.ymeth.2018.03.009