[Biopython-dev] Extended Amino Acid Chains

[João Rodrigues]

Hey Matthew, Rodrigo,

The only problem I see with incorporating such "feature" in Biopython is
that you would need a topology and parameters for the aminoacids and these
are often forcefield dependent. Therefore, the quantity of data to add to
the distribution would be quite big and you'd need someone to keep updating
it as ffs evolve. Or am I seeing this from a completely wrong angle?

Cheers,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



2012/7/24 Rodrigo Faccioli <rodrigo.faccioli at gmail.com>

> 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
> project.
>
> [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
> http://laips.sel.eesc.usp.br
> 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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> >
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