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SHAPE

Posts tagged “SHAPE”.

All3DAIalphavirusbacteriaco-transcriptional RNA foldingenergy landscapesflavivirusmolecular epidemiologynew methodNGSnon-coding RNAOne HealthRNA designRNA folding kineticsRNA-protein interactionRNA-RNA interactionRNA structure conservationRNA structure predictionSHAPEsynthetic biologytoolsViennaRNAvirus bioinformaticsxrRNA
Featured · Publications

Secondary and tertiary structure of the BVDV IRES

This post summarizes what SHAPE-guided modeling and 3D analysis reveal about a pseudoknot in the BVDV internal ribosome entry site and why that matters for IRES function.

Sat 15 May 2021
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Fri 01 July 2016
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Predicting RNA structures from sequence and probing data

This review explains how classical thermodynamic RNA folding models can be improved with chemical probing data, and why that combination remains one of the most reliable routes to biologically useful structure prediction.

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Wed 02 September 2015
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SHAPE-directed RNA folding with ViennaRNA: reactivities as soft constraints

This paper shows how SHAPE-guided RNA folding is implemented in the ViennaRNA Package, comparing three widely used strategies for turning nucleotide reactivities into soft constraints that improve thermodynamic...

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