[Biopython] Code for protein alpha helix prediction

[Frank Kauff]

Thanks everybody!

Now I have plenty of tools to look at - the standalone version of 
psipred certainly fulfills the easy-to-use and quick-to-try-out 
requirements.

Frank

On 04/20/2010 08:16 PM, Steve Darnell wrote:
> 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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