[Biopython] Code for protein alpha helix prediction

[Rodrigo Faccioli]

Hi Frank,

I'm not sure if I understood your question. I'm computer scientist and I'm
researching globular protein structure prediction. In fact, I've studied the
application of Evolutionary Algorithms for it. Therefore, our goals are
different.

if I understood your question, you have a Fasta file of your protein.  So,
you need to communicate with databases such as NCBI, scop and CATH. In this
way, I recommend you use Entrez BioPython module. Other suggestion is the
use of BioPython Blast module.

Sorry if my answer is not what you is looking for.

Thanks,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218


On Tue, Apr 20, 2010 at 11:27 AM, 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?
>
> Thanks in advance,
> Frank
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