[Biodevelopers] [Fwd: [BiO Admin] Could you give me some guidance...]

[Patrick McConnell]

Hi.

Some tools exist for modelling protein sequences, the most popular of which
are Modeller and Threader.  Large protein visualization packages such as
Sybyl have modelling packages built into them that make this sort of thing
pretty easy, but they are pretty pricey.

My senior thesis was entitled "A Web-Integrated Java Workbench for Protein
Modeling".  It was essentially a website that allowed you to run Modeller
on a protein sequenceand visualize the results in a window embedded in the
web page (via Chime or Mage).  From that point, you could decide how to
better model your protein, and you could run modeller again with modified
parameters and template structures.

I never got around to writing it up for publication.  If you are
interested, I can send you the paper (~60 pages) and the code.  If this
appears like a direction you might want to take, then perhaps you can build
on what I have done instead of starting from scratch.

-Patrick McConnell
Duke Bioinformatics Shared Resource
mccon012 at mc.duke.edu






"J.W. Bizzaro" <jeff at bioinformatics.org>@bioinformatics.org on 05/23/2002
11:58:06 AM

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Subject:    [Biodevelopers] [Fwd: [BiO Admin] Could you give me some
       guidance...]



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Subject: [BiO Admin] Could you give me some guidance...
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Date: Thu, 23 May 2002 09:48:02 -0400

Hi,

My name's Rick, I'm a student at the University of
Manchester in England.

I'm just about to start a final year project called "3D
visualisation tools for Bioinformatics"

In this, I aim to work with Bioinformaticians to provide
some graphical aid to their work, eg a tool which converts
a protein string into a 3D protein model.

I was wondering if you might give me some guidance? What
other tools would be useful to a bionformatician? Do you
know of any URL's which might be of aid to me? Thanks.
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