[Biopython] topology of transmembrane proteins in BioPython

[Afonso Duarte]

Hi João

 

>>In Bio.PDB there is not for sure. Bio.Graphics *might* be adapted to deal with such files but I can't tell you how straightforward it can be

 

Thanks ! I will have a look.

 

>>Also, are you by any chance parsing PDBTM files? That could be a useful addition for Bio.PDB.

 

I’m combining and organizing the several groups of  TM pdbs and seq files now… soon I should start parsing them.

 

Thanks! Abraço

 

Afonso 

 

 

De: João Rodrigues [mailto:anaryin at gmail.com] 
Enviada: terça-feira, 20 de Novembro de 2012 15:10
Para: Afonso Duarte
Cc: biopython at lists.open-bio.org
Assunto: Re: [Biopython] topology of transmembrane proteins in BioPython

 

Hey Afonso,

 

In Bio.PDB there is not for sure. Bio.Graphics *might* be adapted to deal with such files but I can't tell you how straightforward it can be. Have a look here:

 

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc200

http://www.bio-cloud.info/Biopython/en/ch15.html

 

Also, are you by any chance parsing PDBTM files? That could be a useful addition for Bio.PDB.

 

Abraço,

 

João

 

2012/11/20 Afonso Duarte <aduarte at itqb.unl.pt>

Dear All,



I´m a newbie in BioPython

I have a list of transmembrane proteins (in XML or txt format that include:
name/sequence number/sequence/ secondary structure prediction/ transmembrane
regions) that I would like to draw a topology picture from.

As I have a large number I would like to implement it in Biopython. Is there
any package/model  that allow to run this task automatically? if not (I
searched but did not found one that would do it), is there a graphical
module that can be adapted to draw such kind of files ? (i.e. just need to
draw rectangles / arrows and connecting lines and allow these to be fully
manipulated)



Thanks!



Afonso




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