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Zeitschriftenartikel

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

MPG-Autoren
http://pubman.mpdl.mpg.de/cone/persons/resource/persons97397

Schudoma,  C.
BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97298

May,  P.
BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97319

Nikiforova,  V.
System Integration, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97467

Walther,  D.
BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Schudoma-2010-Sequence-structure r.pdf
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Zitation

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.


Zitierlink: http://hdl.handle.net/11858/00-001M-0000-0014-233C-4
Zusammenfassung
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.