Atomic accuracy in predicting and designing non-canonical RNA structure

We present a Rosetta full-atom framework for predicting and designing the non-canonical motifs that define RNA tertiary structure, called FARFAR (Fragment Assembly of RNA with Full Atom Refinement). For a test set of thirty-two 6-to-20-nucleotide motifs, the method recapitulated 50% of the experimen...

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Detalles Bibliográficos
Autores principales: Das, Rhiju, Karanicolas, John, Baker, David
Formato: Texto
Lenguaje:English
Publicado: 2010
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854559/
https://www.ncbi.nlm.nih.gov/pubmed/20190761
http://dx.doi.org/10.1038/nmeth.1433
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author Das, Rhiju
Karanicolas, John
Baker, David
author_facet Das, Rhiju
Karanicolas, John
Baker, David
author_sort Das, Rhiju
collection PubMed
description We present a Rosetta full-atom framework for predicting and designing the non-canonical motifs that define RNA tertiary structure, called FARFAR (Fragment Assembly of RNA with Full Atom Refinement). For a test set of thirty-two 6-to-20-nucleotide motifs, the method recapitulated 50% of the experimental structures at near-atomic accuracy. Additionally, design calculations recovered the native sequence at the majority of RNA residues engaged in non-canonical interactions, and mutations predicted to stabilize a signal recognition particle domain were experimentally validated.
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spelling pubmed-28545592010-10-01 Atomic accuracy in predicting and designing non-canonical RNA structure Das, Rhiju Karanicolas, John Baker, David Nat Methods Article We present a Rosetta full-atom framework for predicting and designing the non-canonical motifs that define RNA tertiary structure, called FARFAR (Fragment Assembly of RNA with Full Atom Refinement). For a test set of thirty-two 6-to-20-nucleotide motifs, the method recapitulated 50% of the experimental structures at near-atomic accuracy. Additionally, design calculations recovered the native sequence at the majority of RNA residues engaged in non-canonical interactions, and mutations predicted to stabilize a signal recognition particle domain were experimentally validated. 2010-02-28 2010-04 /pmc/articles/PMC2854559/ /pubmed/20190761 http://dx.doi.org/10.1038/nmeth.1433 Text en Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Das, Rhiju
Karanicolas, John
Baker, David
Atomic accuracy in predicting and designing non-canonical RNA structure
title Atomic accuracy in predicting and designing non-canonical RNA structure
title_full Atomic accuracy in predicting and designing non-canonical RNA structure
title_fullStr Atomic accuracy in predicting and designing non-canonical RNA structure
title_full_unstemmed Atomic accuracy in predicting and designing non-canonical RNA structure
title_short Atomic accuracy in predicting and designing non-canonical RNA structure
title_sort atomic accuracy in predicting and designing non-canonical rna structure
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854559/
https://www.ncbi.nlm.nih.gov/pubmed/20190761
http://dx.doi.org/10.1038/nmeth.1433
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