Article (Scientific journals)
Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.
Schudoma, Christian; May, Patrick; Nikiforova, Viktoria et al.
2010In Nucleic Acids Research, 38 (3), p. 970-80
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Keywords :
Base Sequence; Databases, Nucleic Acid; Internet; Models, Molecular; Nucleic Acid Conformation; RNA/chemistry; Sequence Homology, Nucleic Acid
Abstract :
[en] 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.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Schudoma, Christian
May, Patrick  ;  Max Planck Institute for Molecular Plant Physiology > Bioinformatics
Nikiforova, Viktoria
Walther, Dirk
Language :
English
Title :
Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.
Publication date :
2010
Journal title :
Nucleic Acids Research
ISSN :
1362-4962
Publisher :
Oxford University Press, United Kingdom
Volume :
38
Issue :
3
Pages :
970-80
Peer reviewed :
Peer Reviewed verified by ORBi
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