[Biojava-l] data cleansing scoring functions

bharani kumar phirnee123 at yahoo.com
Wed Nov 19 09:10:14 EST 2003

hello everybody,

we r involved in building a protein docking software
and i would need a suggestion of urs.in this we  r
taking into account 20 scoring functions like
hydrophobicity and stuffs like thatand after that
combine all the scoring functions  to get a optimised
total and plot it against the RMSD of various
conformations resulted by orientation of one protein
over  the other rotationally and translationally.

 Now my question is that does all these 20 scoring
functions are equally important.certainly not.so the
data has to be cleansed and finally i hope we wouild
be left with certain limited number of scoring
functions like 12 or 13.

      so what would be the best way to clean the
data(the scoring  functions).One of my supervisor
suggested that it could be done using matlab by
applying PCA.

      In this regard i need ur  suggestion.


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