How to associate secondary structure to protein sequence
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6 months ago

Hi everybody! I am sruggling to find a way to associate to a vast collection of PDB entries the respective secondary structures. For every protein sequence It would be nice to have every aminoacid associated to the secondary structure, like in the image: enter image description here

I am not looking for secondary structure predictions but for the secondary structure data stored in the PDF files. Does anyone know a program or a Python/R script to rapidly do that on a large amount of PDBs?

secondary python structure pdb database • 273 views
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Entering edit mode
6 months ago
fracarb8 ▴ 300

[dssp][1] does exactly that.

You can run it on it's own, or you can use it as plugin. For example, pyMol support it, and you can process al pdb you need with a python script.

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Thank you!

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