[Bioperl-l] Google summer of code Bio::Structure

Berry Kriesels berry at exisoft.nl
Tue Apr 3 16:24:54 EDT 2012

Dear all,

Currently I am considering applying as a student for the 'google summer 
of code' and would like to contribute to BioPerl via this way.

At the moment I am investigating extending the BioPerl 
Bio::Structure**library in such a way that also some protein modelling 
can be done or at least add a method so one could do a pdb structure 
quality assessment. One way is to do it with the use of online services 
such as for instance Prosaweb (and thus creating a wrapper for this 
service).  Also I could make libraries which one could use to asses the 
phi and psi angles of certain atoms within a PDB file or the distance in 
angstrom among many other coordinate measurements within a protein PDB 
file but also among (comparison) of multiple PDB files. Also adding 
functions such as DOPE (*D*iscrete*O*ptimized*P*rotein*E*nergy) for 
model comparisons is an option. There are tons of options to add. However...

I have a few questions regarding this and hope some of you will be 
willing to answer:

1. As users of BioPerl would you consider extending the current 
Bio::Structure library as a added value or would you rather see effort 
made in different areas.
2. If one would see extension of the current Bio:Structure library as a 
useful project, what would your main interests and wishes be?

Thank you for input and time.

With kind regards,

Msc student Bio-informatics.

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