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  Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling

Schudoma, C., May, P., Nikiforova, V., & Walther, D. (2010). Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. Nucleic Acids Research, 38(3), 970-980. doi:10.1093/nar/gkp1010.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-233C-4 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-233D-2
Genre: Journal Article

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 Creators:
Schudoma, C.1, Author              
May, P.1, Author              
Nikiforova, V.2, Author              
Walther, D.1, Author              
Affiliations:
1BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753303              
2System Integration, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753349              

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Free keywords: 3-dimensional structures structure prediction tertiary structures protein structures database classification visualization molecules search
 Abstract: The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by < 25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

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Language(s): eng - English
 Dates: 2009-11-202010
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
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 Identifiers: ISI: ISI:000274496900029
DOI: 10.1093/nar/gkp1010
ISSN: 1362-4962 (Electronic) 0305-1048 (Linking)
URI: ://000274496900029 http://nar.oxfordjournals.org/content/38/3/970.full.pdf
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Title: Nucleic Acids Research
Source Genre: Journal
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Pages: - Volume / Issue: 38 (3) Sequence Number: - Start / End Page: 970 - 980 Identifier: -