Questions tagged [secondary-structure]

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Unable to execute DSSP algorithm from BioPython

I have the following settings in PyCharm: BioPython is properly installed: dssp_test.py ...
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0answers
15 views

Is "Assignment" a part of the "Prediction" process? [duplicate]

I am talking about secondary structure assignment and secondary structure prediction of proteins. Is "Assignment" a part of the "Prediction" process?
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2answers
130 views

What is the difference between Assignment and Prediction?

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 ...
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0answers
9 views

GOR3 implementation

I (think I) have successfully calculated my GOR3 information function values as a list of float numbers (these numbers already combine self info and directional info). I am however confused about how ...
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1answer
86 views

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?
3
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1answer
77 views

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: ...
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0answers
698 views

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 ...
1
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1answer
78 views

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 ...
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0answers
34 views

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 ...