[Biopython-dev] Extended Amino Acid Chains

Rodrigo Faccioli rodrigo.faccioli at gmail.com
Tue Jul 24 19:01:58 UTC 2012

Hi Mathew,

If I understood your email, I have already implemented it. However, it is
not put into BioPython project yet.In this moment, I don't have time to do
it alone.

In [1] there is an example of my code. In my project I extended the
BioPython classes and created my parser because I had to work with files
and database in same code. Therefore, I believed that it was the best :-).

So, if it is what you wanted, we can work together to put it into BioPython

[1] https://dl.dropbox.com/u/4270818/workingFcfrpStructure.py

Best regards,

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 Structural Bioinformatics
Phone: 55 (16) 3373-8739
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
Personal Blogg - http://rodrigofaccioli.blogspot.com/

On Tue, Jul 24, 2012 at 3:36 PM, Matthew Tien <matthew.tien89 at gmail.com>wrote:

> To whom it may concern,
> I am currently developing a program in Biopython that creates amino acid
> chains from an inputted AA sequence. The program would output a single
> amino acid chain in an extended conformation. Is this something of interest
> to the developers of Biopython?
> I am using basic calculus to calculate the position of the atoms in the
> protein residues and using known protein geometries and database
> information from PDB.org and the Dunbrack group <http://dunbrack.fccc.edu/
> >.
> This program is an extension of my current research in calculating Relative
> Solvent Accessibilities of protein residues.
> Thank you for your time,
> Matthew Tien
> --
> B.S. Biochemistry, University of Texas at Austin
> PhD. student, University of Chicago
> Marcotte Lab and Wilke Group
> alt. Matthew.Tien at yahoo.com
> 361-876-0942
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> Biopython-dev mailing list
> Biopython-dev at lists.open-bio.org
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