[Biopython-dev] Extended Amino Acid Chains

[Rodrigo Faccioli]

Hi Joao,

What I understood about the Tien's idea, your angle is correct.

However, I would like to say is that the use of force-field could be
implemented in biopython through xml files since each xml file represents a
version of ff.

I'm not an expertise in ff. In fact, I have been studying only charmm27
mainly its implementation at gromacs. So, I believe that we can base on
gromacs topology files and create a specific xml file for charmm27, for
example. Maybe create a parser to read these gromacs files.

Furthermore, the use of ff in biopython could be used in other
implementations such as checking the structure.  In this way, we can create
a command like that: check_charmm27(structure). This command can create a
list of errors of structure based on charmm27 ff.

Did I write correctly? This email is an idea only.

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 Wed, Jul 25, 2012 at 4:59 AM, João Rodrigues <anaryin at gmail.com> wrote:

> 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
>> > _______________________________________________
>> > Biopython-dev mailing list
>> > Biopython-dev at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
>> >
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