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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What is happening in the Zuker-Algorithm
I am trying to understand the Zuker Algorithm.
What is happening during initialisation? I know in Nussinov the diagonal is filled with 0s. Are the diagonals filled with infinite energy during Zuker´s ...
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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 ...
M__♦
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How can I calculate the Maximum Ladder Distance (MLD) of ssRNA from Dot-Bracket notation? [duplicate]
The ladder distance (LD) between residue $i$ and residue $j$ is the minimum number of base pairs (created due to secondary structure of the ssRNA) one has to cross when going from $i$ to $j$.
The ...
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Is loss/gain of function reflected in RNA-seq transcript counts?
Do LoF/GoF transcripts count toward the RNA-seq TPM count? Or would these LoF/GoF transcripts only be detected by isoform quantification?
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Explaining the algorithm of RNA folding: what each symbol & value represents?
I need someone to explain to me from the nuts and bolts how algorithms/ maths is used to work out RNA folding. Explain it to me like I am an alien or child.
I am looking at this paper - https://eprint....
M__♦
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What tool RCSB and AlphaFold use to visualize 3D structures?
I would like to implement on a web page a tool to visualize 3D structures like it is for AlphaFold and RCSB.
A couple of examples:
https://www.rcsb.org/3d-view/7KX9
https://alphafold.com/entry/Q5VSL9
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Understanding ViennaRNA RNAdistance scoring table
I'm trying to compare the output of 2 different algorithms of RNA structure prediction
(my implementation of Nussinov vs RNA-mfold algorithm) using the RNAdistance algorithm that is part of ViennaRNA ...
CommunityBot
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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 ...
M__♦
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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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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 ...
M__♦
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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 ...
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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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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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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. ...
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