[BiO BB] hat kinds of data mining techniques have been using indrug discovery and drug delivery

[Mike Marchywka]

I don't really have anything insightful to say directly regarding your 
question but I will point
out that there are good case studies on pubmed- protease and polymerase 
targeting, or
if you prefer kinases, should keep you busy for a while :) As far as 
delivery,
lots of nano stuff, not sure on tools.

I did want to mention that I have been amazed at the ( apparent) lack of 
some simple
tools however. While it is quite possible I missed some, I have had to write
a lot of scripts and c++ code to augment the Affymetrix annotations. Much of
this is just the novel idea of using a computer to automate data processing 
rather
than require a user to appreciate someone's nice web page for every protein
he wants to investigate. However, then there are things like string 
correlators
that execute in reasonable time, programmable ribosomes, format converters 
etc.

I suppose I could have looked more carefully at conserved domain servers or
bioperl packages to address various parts of the problem but so far I think
I've done better with my own approach.  I'm not sure I have exploited all
the online tools- I only really use blast and eutils to download batches
of proteins or nucleotides - but I do know that perl, at least under cygwin,
was simply too slow to do anything of any size. I ended up writing my own
c++ string manipulation stuff ( even here under cygwin the STL string
classes were just too slow and I created objects that manipulate c-style
strings ). Even using grep+sed to convert to fasta files was quite slow
( although I think this turned out to be mostly a problem using
cygwin to pipe results - the console buffering seems to be the problem).
I don't want to sound negative on cygwin- you just can't do this with
BAT files and it is hard to get reasonable performance on top of windoze-
but I'm not sure if that is creating some of the limitations.

Don't know if any of that helps but I am curious if anyone has similar or
contrasting observations.

Thanks.



Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165
404-788-1216 (C)<- leave message
989-348-4796 (P)<- emergency only
marchywka at hotmail.com





>From: "Xue Li" <me.lixue at gmail.com>
>Reply-To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: bio_bulletin_board at bioinformatics.org
>Subject: [BiO BB] hat kinds of data mining techniques have been using 
>indrug discovery and drug delivery
>Date: Tue, 17 Jul 2007 13:33:59 -0500
>
>Hello all,
>
>I was wondering what kinds of data mining techniques have been using in 
>drug
>discovery and drug delivery? It would be much appreciated if you could 
>offer
>me some resources to find it out. Millions of thanks.
>
>As far as I know, classification techniques are used in protein-protein
>interface prediction, and RNA-  , DNA-  interface prediction.
>Are optimization techniques used? How about regression techniques?
>
>--
>Li Xue
>Bioinformatics and Computational Biology program @ ISU
>515-520-1676
>Ames, IA 50010
>_______________________________________________
>General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

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