Dear Joe,
Thanks, what you explained is exactly right. But I would like to visualize
only Hub/ Non-Hub proteins out of the PPI network. How could the tool can
discriminate proteins into Hub and Non-Hub? Have you used any computational
approach?
Lijo
On Fri, Apr 18, 2008 at 6:18 PM, Joe Ivanic [Contractor, Foreign National] <
[EMAIL PROTECTED]> wrote:
> Note that an equivalent e-mail with attachments is awaiting moderator
> approval. I include original text only below:
>
> ---
>
> I believe the person wishes to view protein-protein interaction (PPI)
> networks using Jmol. I have been doing this for quite some time.
>
> Basically a PPI is just a bunch of proteins (nodes) and interactions
> (edges) between them. They can be interpreted as networks. However, to view
> them one must come up with a geometry. I have treated PPI networks as sort
> of big molecules and then optimized node coordinates for a simple "Energy"
> objective function (my background is quantum chemistry).
>
> Of course, some proteins (nodes) will have more interactions than others,
> and the ones that have the most, by far, are called hubs.
>
> I include a .gpr and script file (which reads in the .gpr) and colors some
> hubs red, while leaving the other nodes and edges grey. I have actually made
> a movie file from this by rotating by a degree, taking a snapshot, etc. The
> file uses Jmol to view the PPI network of E. coli determined from a
> particular experiment.
>
> Joe
>
>
> ---
>
> Dr. Joe Ivanic - Contractor, Foreign National
> Scientist
> Biotechnology HPC Software Applications Institute
> ATTN: MCMR-TT
> Building 363, Miller Drive
> Ft. Detrick, MD 21702-5012
>
> Voice: (301) 619 1976
> Fax: (301) 619 1983
>
> -----Original Message-----
> From: [EMAIL PROTECTED] [mailto:
> [EMAIL PROTECTED] On Behalf Of Angel Herraez
> Sent: Friday, April 18, 2008 8:34 AM
> To: [email protected]
> Subject: Re: [Jmol-users] Hub and Non-Hub
>
> Hi lijo
>
> Could you please explain waht do you mean by "hub" and "hub protein"?
> Best if you provide an example file
>
>
>
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--
Manger Projects,
SooryaKiran Bioinformatics,
Centre for Bioinformatics,
University of Kerala, India.
+91 4714060948(off)
+91 9446515705(res)
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