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

Xue Li me.lixue at gmail.com
Wed Jul 18 13:52:29 EDT 2007

Thank you, Mike, for your such long help :P

I am just a beginner in Data mining and bioinformatics, so I am sure about
the problems with cygwin and perl. I know that there is Bio++ where some C++
library for bioinformatics are be found.

Hope it will help.


On 7/17/07, Mike Marchywka <marchywka at hotmail.com> wrote:
> 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
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> _________________________________________________________________
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Li Xue
Bioinformatics and Computational Biology program @ ISU
Ames, IA 50010

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