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

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 a

SUBMITTER: Schudoma C 

PROVIDER: S-EPMC2817452 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature