[Biopython] Code for protein alpha helix prediction

[Steve Darnell]

Frank,

One of the most accurate (and popular) algorithms is PSIPRED.  A
stand-alone command line version is available:
http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/

If memory serves, it requires a local installation of blast and the nr
database.  A position weight matrix generated from PSI-BLAST acts as
input to a neural network, which makes the secondary structure
predictions.

The Rosetta Design group had a poll last year of people's favorite
tools.  There are plenty of others to try if PSIPRED doesn't meet your
needs.

http://rosettadesigngroup.com/blog/456/fairest-secondary-structure-predi
ction-algorithm/

I am not a PSIPRED developer, just a satisfied user.

Regards,
Steve

-----Original Message-----
From: biopython-bounces at lists.open-bio.org
[mailto:biopython-bounces at lists.open-bio.org] On Behalf Of Peter
Sent: Tuesday, April 20, 2010 10:43 AM
To: Frank Kauff
Cc: BioPython Mailing List
Subject: Re: [Biopython] Code for protein alpha helix prediction

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
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