Questions tagged [secondary-structure]

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Is there any python module to assign secondary structures which includes both Polyprolene region as well as individual strand as well?

I wanted to assign secondary structure to set of pdb files. However, DSSP and STRIDE cannot assign for single peptides if it is falling inside single long beta strand or polyprolene region as it does ...
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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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which secondary structure assignment algorithm is used by PDB?

older releases of PDB used to specify DSSP as the 2ary structure assignment algorithm used in PDB, right now no algorithm is explicitly stated. Where can I find a reference for it in the database?
raysas's user avatar
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Is there a software that extract molecular descriptors of single stranded RNAs secondary structure from dot bracket notation in nucleotide resolution?

I want to generate descriptors from dot bracket notations of single stranded RNA/DNA secondary structures. So far i have come across this paper:
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RNA folding at specific temperature with ViennaRNA in python

I am trying to get dot-bracket-notations of single stranded RNA via the ViennaRNA python package ( at different temperatures. I have read in the docs (https://www....
gojih's user avatar
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Visualize RNA co-folded secondary structure with Python

I would like to visualize the secondary structure of co-folded RNA strands in Python, preferably in a Jupyter notebook. What are the recommended tools? Can anyone provide an example?
Ita's user avatar
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Sequence format: grouping sequences within a flat file

Is there a sequence format allowing multiple sequences to be grouped across a flat file? The specific application is stacking separate nucleotide sequences against a given RNA secondary structure. To ...
M__'s user avatar
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Program for SOV calculation

Are there any programs (web server or installable) out there to calculate segment overlap score (SOV) for protein secondary structures? Thanks
Balint Biro's user avatar
2 votes
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Chou-Fasman Method Overlapping Regions Problem - Secondary Structure Prediction

According to the Chou-Fasman method, when there is an overlapping region on the amino acid sequence, we compare the scores of alpha-helix and beta-sheet and chose the highest one. Let's say I have ...
didar's user avatar
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Unable to execute DSSP algorithm from BioPython

I have the following settings in PyCharm: BioPython is properly installed: ...
user366312's user avatar
3 votes
2 answers

What is protein secondary structure assignment?

I am absolutely new to Structural Bioinformatics (I only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using ML. When it comes ...
user366312's user avatar
1 vote
1 answer

Searching for proteins by primary and secondary structure

I need to find peptides/proteins with a certain sequence of amino acids in a certain type of secondary structure. For example, "ALA PHE GLY" in alpha-helix. Is there any tool that does that?
user75619's user avatar
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protein secondary structure matching/comparison scoring

I want to compare two secondary structures of aligned proteins. I do not know exactly how to do it well. Example: ...
MTG's user avatar
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How to plot a 2D RNA structure in python using dot-bracket input?

I need some help with forgi library for visualisation of RNA secondary structure. I have an RNA sequence and dot-bracket notation of the secondary structure and I would like to plot 2D graph like ...
kitsune_breeze's user avatar
1 vote
1 answer

Which is the amino acids classification when analyzing the solvent accessibility of a protein?

I came across an article which has defined 3 categories: Buried [A, L, F, C, G, I, V, W], Exposed [ R, K, Q, E, N, D] and Intermediate [M, S, P, T, H, Y] when analyzing the solvent accessibility of a ...
girl101's user avatar
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Which secondary structure prediction algorithms don't query the PDB/DSSP for known homologous sequences?

There are several secondary structure prediction algorithms. I am interested in the algorithms which predict secondary structure without accessing the PDB to cheat by using the DSSP or STRIDE entry ...
Aalawlx's user avatar
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