The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs
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- 作者：Lorena G. Parleaa ; lorenan@bgsu.edu" class="auth_mail" title="E-mail the corresponding author ; Blake A. Sweeneya ; bsweene@bgsu.edu" class="auth_mail" title="E-mail the corresponding author ; Maryam Hosseini-Asanjanc ; Craig L. Zirbelb ; zirbel@bgsu.edu" class="auth_mail" title="E-mail the corresponding author ; Neocles B. Leontisc ; leontis@bgsu.edu" class="auth_mail" title="E-mail the corresponding author
- 关键词：HL ; Hairpin Loop ; IL ; Internal Loop ; 3WJ ; 3-way Junction ; 4WJ ; 4-way Junction ; MHJ ; Multi-Helix Junction ; 2D structure ; Secondary structure ; PDB ; Protein Data Bank ; NDB ; Nucleic Acid Database ; WC ; Watson-Crick ; non-WC ; non-Watson-Crick ; BP ; basepair ; NR ; Non-redundant ; nt ; nucleotide ; S/R ; Sarcin/Ricin ; mRNA ; messenger RNA ; tRNA ; transfer RNA ; rRNA ; ribosomal RNA ; SSU ; small ribosomal subunit ; LSU ; large ribosomal subunit
- 刊名：Methods
- 出版年：2016
- 出版时间：1 July 2016
- 年：2016
- 卷：103
- 期：Complete
- 页码：99-119
- 全文大小：1892 K
文摘
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Up to 40% of nucleotides in structured RNAs are in hairpin, internal and junction loops.
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Loops are structured by non-Watson-Crick base-pairing and -stacking interactions.
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RNA 3D motifs found in loops can be extracted and clustered into motif groups.
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Many RNA 3D motif geometries are modular and recurrent with similar non-WC pairing.
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Corresponding motifs in homologous structures frequently conserve 3D structure.