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Nat Methods. 2010 Apr;7(4):291-4. doi: 10.1038/nmeth.1433. Epub 2010 Feb 28.

Atomic accuracy in predicting and designing noncanonical RNA structure.

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1
Departments of Biochemistry and Physics, Stanford University, Stanford, California, USA. rhiju@stanford.edu

Abstract

We present fragment assembly of RNA with full-atom refinement (FARFAR), a Rosetta framework for predicting and designing noncanonical motifs that define RNA tertiary structure. In a test set of thirty-two 6-20-nucleotide motifs, FARFAR recapitulated 50% of the experimental structures at near-atomic accuracy. Sequence redesign calculations recovered native bases at 65% of residues engaged in noncanonical interactions, and we experimentally validated mutations predicted to stabilize a signal recognition particle domain.

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PMID:
20190761
PMCID:
PMC2854559
DOI:
10.1038/nmeth.1433
[Indexed for MEDLINE]
Free PMC Article

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