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7 votes
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What is protein secondary structure assignment?

To make it crystal clear (and make than pun): Assignment: a 3D structure is known and the residues are assigned a secondary structure ...
Matteo Ferla's user avatar
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4 votes
Accepted

Why do we need seondary structure detection algorithms?

Right, that's easy PDB is strictly experimentally derived structures, for example crystal structures or NMR. There are at least three very good reasons, There are billions of proteins. Even small ...
M__'s user avatar
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3 votes
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How can I detect secondary structures in a protein using a hydrogen bond detection algorithm?

Firstly, of course, I should point out that there is software that already does this DSSP and Stride, among others (see a partial list here : https://2struccompare.cryst.bbk.ac.uk/methods.php) However,...
gilleain's user avatar
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3 votes
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Searching for proteins by primary and secondary structure

Your request is rather specific, so there is no tool... It is a straightforwards request though. I'd impose the requirement that the structures be solved and no predicted secondary structure. You can ...
Matteo Ferla's user avatar
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2 votes
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Sequence format: grouping sequences within a flat file

An unmapped SAM file format allows for read groups. You can use samtools import to create unmapped SAM files from FASTQ files: ...
gringer's user avatar
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2 votes
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Which is the amino acids classification when analyzing the solvent accessibility of a protein?

There is some confusion in the question. Solvent accessibility of a residue, i.e. the area accessible to the solvent (water), depends on the 3D structure of the protein. It's not a property of an ...
marcin's user avatar
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1 vote

What is protein secondary structure assignment?

Answer from @jan-wilamowski, converted from comment: That second paper seems to distinguish between the known data that is used for ML training (i.e. amino acid sequences are assigned some secondary ...
1 vote

RNA folding at specific temperature with ViennaRNA in python

I think that the "Global Variables" section of the docs describes this: For the Python interface(s) SWIG places global variables of the C-library into an additional namespace cvar. For ...
Maximilian Press's user avatar
1 vote

Visualize RNA co-folded secondary structure with Python

... . I know both aspects of this question and I'm not aware of an interactive Python package using e.g. iPython magic commands that will do this. The thing you could try is ...
M__'s user avatar
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1 vote

Chou-Fasman Method Overlapping Regions Problem - Secondary Structure Prediction

Sure, an isolated residue has a ψ and φ angles, so you could technically have an isolated residue in a given SS conformation, but that does not mean much if its neighbours' backbones aren't in that ...
Matteo Ferla's user avatar
  • 4,244
1 vote

Unable to execute DSSP algorithm from BioPython

Ok so this might not provide a solution, but here's a couple things someone might find useful; First, Biopython does not automatically contain DSSP, which you have to download as mentioned in the ...
kormi's user avatar
  • 43
1 vote

Unable to execute DSSP algorithm from BioPython

This looks like a python problem and not a “biopython”problem. Check your file structures. Try giving a full path for 16pk.pdb These might help. https://stackoverflow.com/questions/17658856/why-am-i-...
jayesh saha's user avatar
1 vote
Accepted

protein secondary structure matching/comparison scoring

Hey i solve this simply by use of SOV alghoritm. https://www.researchgate.net/publication/319526145_A_modified_definition_of_Sov_a_segment-...
MTG's user avatar
  • 147
1 vote

How to plot a 2D RNA structure in python using dot-bracket input?

One way simply is to use VARNA, here is a link ... https://varna.lri.fr. This is well known for its power to view secondary structure (e.g. its in Jalview). It is generally considered the best viewer ...
M__'s user avatar
  • 12.6k
1 vote

How to plot a 2D RNA structure in python using dot-bracket input?

I wrote a function to do that a while ago, maybe it helps. It only works with dot-bracket notation, and it turns it into ordered pairs which then you can easily plot. ...
nquinoneso's user avatar

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