I have a large list of protein accession numbers (which I could convert to another identification type) that were identified as binding partners of my protein of interest. I would like to draw out an analysis of the hydrophobicity, beta-sheet, and alpha-helix content of these proteins. I've found the ExPASY ProtScale tool, which is pretty much what I'm after, but to go through this list and export these data for this many proteins will take me... a very long time...
Does anyone know of a tool that could help me?
If you use python, I would suggest you could use a python package called mdtraj to extract the secondary information if the 3D coordination of the proteins are available.
Thanks Pritam Kumar Panda
I'll look into both of those and see how I go :) . And Liangzhen Zheng I'm not experienced with python, but I may be able to get some help from a colleague that is... Thank you!
Maybe this webserver will be of interest? http://volpes.univie.ac.at/
It was published recently here: https://academic.oup.com/nar/article/47/W1/W632/5494750
http://provean.jcvi.org/index.php
http://crdd.osdd.net/raghava/copid/help.html
Simple batch run of "stride" program will do (Frishman & Argos 1995). Here is a pseudo-code:
1. Loop PDB entries
2. wget PDB entry and run stride with the file.
3. parse the outcome to obtain secondary structures and SASA.
4. Divide by SASA of G-X-G to get hydrophobic scale (Lee & Richards 1971).
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