[Biojava-dev] GSoC

[Serdar Ozsezen]

Dear all,

After my talks with my professor, I was advised to change the project
subject directly to molecular dynamics analysis which is directly related
to full scale protein dynamics. This would be a package which contains DCD
files reader (DCD is a common extension of the binary files which are
created by MD simulations), DCD to PDB converter (PDB files that contain
each frame of simulation just like NMR models). Also it would have the
tools to do analysis on MD trajectories. These analysis methods could
include mean square fluctuations of residues
<http://en.wikipedia.org/wiki/Root_mean_square_fluctuation>, auto-correlations
of residues <http://en.wikipedia.org/wiki/Autocorrelation>,
cross-correlations <http://en.wikipedia.org/wiki/Cross-correlation>
(presentation of them as heatmaps, if I can find good tools to create these
charts easily in Java) and visualizations of these analysis. I think this
would be a better start for protein dynamics analysis in BioJava.

Also these methods are much better known in comparison and it could really
increase my chance to find mentors as well.

So I would be grateful if you could kindly change the BioJava part in OBF
list from Gaussian Network Model to Molecular Dynamics Analysis package.

Best regards,

Serdar

-- 
Serdar Özsezen

Research Assistant

*Polymer Research Center*
*Bogazici University, Bebek, Istanbul*
http://safir.prc.boun.edu.tr/prcw/people/serdar-ozsezen/
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