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PMID: 20190761 Published · ppublish English Journal Article

Atomic accuracy in predicting and designing noncanonical RNA structure.

Nature methods ·Vol. 7 ·No. 4 ·2010-04-00 ·Pages 291-4

Das R, Karanicolas J, Baker D

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.

MeSH Terms
Base Sequence/genetics Models, Chemical Models, Genetic Models, Molecular Mutation Nucleic Acid Conformation RNA/chemistry,genetics Signal Recognition Particle Thermodynamics
Chemicals
Signal Recognition Particle RNA
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Das Rhiju
Departments of Biochemistry and Physics, Stanford University, Stanford, California, USA. [email protected]
Karanicolas John
Baker David
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Article Info
Journal
Nature methods
Abbr.
Nat Methods
ISSN
1548-7105
DOI
10.1038/nmeth.1433
Email
[email protected]
Published
2010-04-00
Epub
2010-00-28
Pages
291-4
Language
English
Region
United States
NLM ID
101215604
PMCID
PMC2854559
Subset
IM
Grants
NIGMS NIH HHS · P20 GM076222 · United States
NIGMS NIH HHS · P20 GM076222-03S1 · United States
Corrections
CommentIn
PMID: 20354517
External Links
PubMed source DOI: 10.1038/nmeth.1433 PMC Full Text View journal details
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