Questions tagged [rna-structure]

The three-dimensional structure of RNA. How to visualise it, determine it from data, analyse its implications.

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RNA loop prediction: how to interpret differences between RNAfold and Mfold?

I'm trying to find out the structure of a conserved ITS loop. As my initial prediction (using only bases homologous to those present in the loop in a closely-related species) was fairly low-scoring, I ...
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40 views

Protein misfolding

I am looking for literature on protein and RNA mis-folding. I am on the computational/biophysics side, and what interests me are the practical applications: diseases caused by misfolding, drug ...
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130 views

Coronavirus RNA structures?

Is there anything known about the RNA structures of coronaviruses? More specifically - do they have any interesting known structures in the translatable region, like RRE of HIV or the double loops in ...
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41 views

Practical use of RNA structure

I have spent some time studying RNA structures. While there is a range of interesting phenomena and functions that certainly deserve understanding from the scientific point of view, I have never ...
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63 views

How is that ensemble Free energy is lower than the MFE in RNAfold from ViennaRNA

In the tutorial of RNAfold it states, RNAfold reads RNA sequences from stdin, calculates their minimum free energy (MFE) structure, prints the MFE structure in ...
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57 views

JSmol - hide “JSmol” logo

I'm using JSmol for my SimRNAweb server. I would like to hide "JSmol" logo from all small visualizations that I have there. I would like to just put information about JSmol under the panel in text.
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Do any publicly available databases detail protein structure and functional domains?

I am interested in finding a database that takes a gene or protein name as input (possibly with the option to specify transcript) and gives information about the protein's functional domains in terms ...
6
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1answer
281 views

How to find hairpin loop structure in a large set of long non coding RNA transcripts

I have done de novo assembly of pair end raw read sequences and resulted transcripts sequences were separated based on coding potential into two categories: long non-coding RNA transcripts and coding ...
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633 views

How to extract RNA sequence and secondary structure restrains from a PDB file

I'm trying to find a programmatic way to automatically extract the following information from a PDB file: RNA sequence Secondary structure restraints in bracket format, e.g. ...