RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools
نویسندگان
چکیده
منابع مشابه
RNA StrAT : RNA Structure Analysis Toolkit
Summary: We present a web server dedicated to the comparison of RNA secondary structures. This server allows to compare pairs of RNA secondary structures and to search, for a given RNA secondary structure, RNA genes with similar structures in a large database of RNA structures. The comparison and search are performed using an edit distance algorithm that considers a wide range of edit operation...
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RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine m...
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We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The ...
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The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challen...
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The view of RNA as simple information transfer molecule has been continuously challenged since the discovery of ribozymes, a class of RNA molecules with enzyme-like function. Moreover, the recent discovery of tiny RNA molecules such as RNAs and small interfering RNA, is transforming our thinking about how gene expression is regulated. Thus, RNA molecules are now known to carry a large repertory...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2019
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkz1108