[Bioperl-l] Google summer of code Bio::Structure
berry at exisoft.nl
Tue Apr 3 16:24:54 EDT 2012
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.
More information about the Bioperl-l