Check if sequence is cytosol-facing?

Question

[ngarber]

I've got a list of proteins with Ensembl ID, protein name, and a motif found by an algorithm I ran in another Python script. For each entry, I need to check:

1. If the protein is a transmembrane protein
2. If it's a transmembrane protein, whether the motif is in the cytosol-facing part or not

So I need to write a script that somehow requests the protein sequence by Ensembl ID, receives topology information, and then checks where the motif is, returning the topological location.

How do I do that? Not sure how to work with topology in Python scripts... thanks in advance for any help you can give!

Answer 1

[Mensur Dlakic]

Not sure about doing it in python, but here is a website and from there you can also download a standalone program:

http://cctop.ttk.hu/