Lijo,
For a particular network I order the proteins by degree (highest to lowest),
and then optimize a "geometry" and generate a corresponding .gpr file (in which
you can specify which edges, or "bonds", are to be visualized. I then use Jmol
commands to specify certain nodes and edges and color them according to some
scheme. For complicated color schemes, such as protein function, I write codes
to generate Jmol scripts.
Once the e-mail with the attachments is approved, you will see an example of
this.
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
________________________________
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of lijo skb
Sent: Friday, April 18, 2008 9:00 AM
To: [email protected]
Subject: Re: [Jmol-users] Hub and Non-Hub
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]<mailto:[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]> [mailto:[EMAIL
PROTECTED]<mailto:[EMAIL PROTECTED]>] On Behalf Of Angel Herraez
Sent: Friday, April 18, 2008 8:34 AM
To: [email protected]<mailto:[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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