[Biopython] Code for protein alpha helix prediction

[Peter]

On Tue, Apr 20, 2010 at 3:27 PM, Frank Kauff <fkauff at biologie.uni-kl.de> wrote:
> Hi all,
>
> I've recently been asked to help with screening protein sequences for
> certain features, something I don't really know much about... Yet!
>
> My questions: Is there some code in Biopython that allows for a quick check
> whether an amino acid sequece is likely to be a alpha helix? Couldn't find
> any. Or is there an algorithm that could be straightforwardly implemented in
> python, or a commandline tool that could be called from within a python
> script?

Hi Frank,

There are lots of tools for predicting secondary structure (alpha helices,
beta sheets etc) both de novo, and guided by reference sequences with
known structures. Some of these are online web services.

I'm pretty sure there is nothing for this built into Biopython, so for scripting
this for a large number of sequences then (as you have also suggested),
my first approach would be to look for command line tools which you could
call from Python. I've never needed to do this myself, and have no specific
recommendations regarding which tools to try first.

If you do find some useful algorithms which could easily be implemented
in Python, they could be worth including - maybe under Bio.SeqUtils?

Peter