[BiO BB] bio game / bioinformatics game /fun

[Kalidas Yeturu]

Hi Mike and Deepan,
  My suggestion is OpenGL, though I have not experimented much (but for
sample programs) is a feasible idea?

Further, regarding the gaming software - it can be an interactive graphics
s/w (JRE/Jmol) like shooting a ligand
at a binding site, or traversal of a peptide in a galaxy of hydrophobic
bombs etc. ;-)
In such a scenario I would like to inform that  I had culled out segments of
code from autodock-3.0
and created a C-stand-alone-module to suite to applying torsions at specific
bonds and generating PDB
formatted-output after each torsion. So this module can take care of any
dynamics to be incorporated
in graphics..

Regards
Kalidas. Y

On 12/22/06, Mike Marchywka <marchywka at hotmail.com> wrote:
>
> Actually, does someone know of an opensource or free graphics rendering
> program
> that can be used with scripts for prototyping these kinds of ideas?
>
> I downloaded this thing:
> http://www.csim.com/models/vpt/viewer/format2.html
> and wrote some perl to take the pdb file for a
>
> COMPND    Ptp1b With The Catalytic Cysteine Oxidized To A
> COMPND   2 Sulfenyl-Amide Bond
>
> and display selected atoms using the above viewer. It worked ok- I could
> put the viewpoint at the oxidized cysteine and see what other things
> could still get to the residue. However, before investing a lot of time
> in scripts to support this viewer, I thought someone here may have
> some better suggestions. It doesn't have to be fancy but transparency and
> shadows would be nice ( being able to move lightsources and view point
> interactively with tolerable CPU usage a big plus ).
>
>
> Thanks.
>
>
>
>
> ( note new address as of 10-06)
> Mike Marchywka
> 586 Saint James Walk
> Marietta GA 30067-7165r
> ( NOTE MORE NEWER  NUMBER )
> 404-788-1216 (C)<- leave message
> 989-348-4796 (P)<- emergency only
>
>
>
>
>
> >From: Dan Bolser <dmb at mrc-dunn.cam.ac.uk>
> >Reply-To: "General Forum at Bioinformatics.Org"
> ><bio_bulletin_board at bioinformatics.org>
> >To: codeshepherd at gmail.com,"General Forum at Bioinformatics.Org"
> ><bio_bulletin_board at bioinformatics.org>
> >Subject: Re: [BiO BB] bio game / bioinformatics game /fun
> >Date: Fri, 22 Dec 2006 09:13:58 +0100
> >
> >Deepan wrote:
> >>Does anyone have any interesting ideas about games wrt to
> >>biology/bioinformatics ? If you have any good ideas, or pointers I would
> >>like to create a web
> >>game just for fun. I was thinking about some kind of game to program a
> >>vector and infect a culture or designing of vectors or bacterial genome
> >>blah blah blah..
> >>
> >>
> >
> >Sim 'virus' or Sim 'bug' - that would be really great!
> >
> >How about a 'first person perspective' view of protein structure? Take
> Doom
> >/ Quake and map the floor of the game onto the surface of your favorite
> >structure. Then you could explore the active site 'on foot' and carry a
> >ligand into the receptor to get to level 2. (Watch out for the slippery
> >hydrophobic cluster!)
> >
> >
> >
> >
> >
> >
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-- 
Kalidas Y
http://ssl.serc.iisc.ernet.in/~kalidas